From 3bc22066da552482fdbfbbfd22da1a5081a15a53 Mon Sep 17 00:00:00 2001 From: Thiseas Christos Lamnidis Date: Tue, 25 Jul 2023 15:09:08 +0200 Subject: [PATCH 1/6] Add 2021_Saag_EastEuropean ssf --- .../2021_Saag_EastEuropean.ssf | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 packages/2021_Saag_EastEuropean/2021_Saag_EastEuropean.ssf diff --git a/packages/2021_Saag_EastEuropean/2021_Saag_EastEuropean.ssf b/packages/2021_Saag_EastEuropean/2021_Saag_EastEuropean.ssf new file mode 100644 index 0000000..1d21c75 --- /dev/null +++ b/packages/2021_Saag_EastEuropean/2021_Saag_EastEuropean.ssf @@ -0,0 +1,48 @@ +poseidon_IDs udg library_built notes run_accession study_accession sample_accession sample_alias secondary_sample_accession first_public last_updated instrument_model library_layout library_source instrument_platform library_name library_strategy fastq_ftp fastq_aspera fastq_bytes fastq_md5 read_count submitted_ftp +BER001 minus ds n/a ERR5032504 PRJEB40698 SAMEA7753461 utigBER001 ERS5500799 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/004/ERR5032504/ERR5032504.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/004/ERR5032504/ERR5032504.fastq.gz 292514298 fd022f8ab9f4cab7ca30e38ca9084618 8039814 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032504/WG25chr_utigBER001_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032504/WG25chr_utigBER001_2_merge_remdup_realign_MQ10.bam.bai +PES001 minus ds n/a ERR5032506 PRJEB40698 SAMEA7753463 utigPES001 ERS5500801 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/006/ERR5032506/ERR5032506.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/006/ERR5032506/ERR5032506.fastq.gz 9307234669 78bac5a651404ab19c84e088cc75ac33 298730894 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032506/WG25chr_utigPES001_3_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032506/WG25chr_utigPES001_3_merge_remdup_realign_MQ10.bam.bai +BOL001 minus ds n/a ERR5032507 PRJEB40698 SAMEA7753464 utigBOL001 ERS5500802 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/007/ERR5032507/ERR5032507.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/007/ERR5032507/ERR5032507.fastq.gz 254062865 8a04181b296cd61da74b101e8f79be7f 6722049 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032507/WG25chr_utigBOL001_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032507/WG25chr_utigBOL001_1_merge_remdup_realign_MQ10.bam.bai +HAN001 minus ds n/a ERR5032512 PRJEB40698 SAMEA7753469 utigHAN001 ERS5500807 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/002/ERR5032512/ERR5032512.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/002/ERR5032512/ERR5032512.fastq.gz 695002 33004163ca4ae2f01a8252825a804f67 18026 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032512/WG25chr_utigHAN001_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032512/WG25chr_utigHAN001_1_merge_remdup_realign_MQ10.bam.bai +HAN003 minus ds n/a ERR5032514 PRJEB40698 SAMEA7753471 utigHAN003 ERS5500809 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/004/ERR5032514/ERR5032514.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/004/ERR5032514/ERR5032514.fastq.gz 2666179 b0bbfdee498c1cc05377668fd04783c5 76688 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032514/WG25chr_utigHAN003_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032514/WG25chr_utigHAN003_1_merge_remdup_realign_MQ10.bam.bai +BOL002 minus ds n/a ERR5032508 PRJEB40698 SAMEA7753465 utigBOL002 ERS5500803 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/008/ERR5032508/ERR5032508.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/008/ERR5032508/ERR5032508.fastq.gz 261433646 97c1b87c1f49b580d101feaa32bd4ddc 6937496 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032508/WG25chr_utigBOL002_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032508/WG25chr_utigBOL002_2_merge_remdup_realign_MQ10.bam.bai +IVA001 minus ds n/a ERR5032516 PRJEB40698 SAMEA7753473 utigIVA001 ERS5500811 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/006/ERR5032516/ERR5032516.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/006/ERR5032516/ERR5032516.fastq.gz 2853025151 30e6e84734bc384d987fbf577b44faab 78943389 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032516/WG25chr_utigIVA001_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032516/WG25chr_utigIVA001_2_merge_remdup_realign_MQ10.bam.bai +HAL001 minus ds n/a ERR5032511 PRJEB40698 SAMEA7753468 utigHAL001 ERS5500806 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/001/ERR5032511/ERR5032511.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/001/ERR5032511/ERR5032511.fastq.gz 2868371016 f7b4fbce6e73b1dc80e52cab10e9383f 82536904 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032511/WG25chr_utigHAL001_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032511/WG25chr_utigHAL001_2_merge_remdup_realign_MQ10.bam.bai +HAN002 minus ds n/a ERR5032513 PRJEB40698 SAMEA7753470 utigHAN002 ERS5500808 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/003/ERR5032513/ERR5032513.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/003/ERR5032513/ERR5032513.fastq.gz 2742740251 455ed9b910e32c4604949b2398bae950 78348821 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032513/WG25chr_utigHAN002_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032513/WG25chr_utigHAN002_2_merge_remdup_realign_MQ10.bam.bai +MIL002 minus ds n/a ERR5032518 PRJEB40698 SAMEA7753475 utigMIL002 ERS5500813 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/008/ERR5032518/ERR5032518.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/008/ERR5032518/ERR5032518.fastq.gz 258025479 3d0e4ee9349683b9e887eb2121fddc6a 7014599 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032518/WG25chr_utigMIL002_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032518/WG25chr_utigMIL002_2_merge_remdup_realign_MQ10.bam.bai +NAU001 minus ds n/a ERR5032520 PRJEB40698 SAMEA7753477 utigNAU001 ERS5500815 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/000/ERR5032520/ERR5032520.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/000/ERR5032520/ERR5032520.fastq.gz 3530555063 1829c1c9a54102e2568480e8923baee1 105110027 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032520/WG25chr_utigNAU001_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032520/WG25chr_utigNAU001_2_merge_remdup_realign_MQ10.bam.bai +NAU002 minus ds n/a ERR5032521 PRJEB40698 SAMEA7753478 utigNAU002 ERS5500816 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/001/ERR5032521/ERR5032521.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/001/ERR5032521/ERR5032521.fastq.gz 2392570791 309d19e8c4fb46c9774dd81aea833248 68076352 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032521/WG25chr_utigNAU002_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032521/WG25chr_utigNAU002_2_merge_remdup_realign_MQ10.bam.bai +HAN004 minus ds n/a ERR5032515 PRJEB40698 SAMEA7753472 utigHAN004 ERS5500810 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/005/ERR5032515/ERR5032515.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/005/ERR5032515/ERR5032515.fastq.gz 2637269727 2ea69a40473fd393ad09afba73bc559e 74291359 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032515/WG25chr_utigHAN004_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032515/WG25chr_utigHAN004_2_merge_remdup_realign_MQ10.bam.bai +RDT002 minus ds n/a ERR5032531 PRJEB40698 SAMEA7753488 utigRDT002 ERS5500826 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/001/ERR5032531/ERR5032531.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/001/ERR5032531/ERR5032531.fastq.gz 47712640 77f895fde4cc3a1bdf1379fdcacf6785 1366083 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032531/WG25chr_utigRDT002_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032531/WG25chr_utigRDT002_1_merge_remdup_realign_MQ10.bam.bai +TIM009 minus ds n/a ERR5032541 PRJEB40698 SAMEA7753498 utigTIM009 ERS5500836 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/001/ERR5032541/ERR5032541.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/001/ERR5032541/ERR5032541.fastq.gz 12080082 4074e7ffb09466c087a60c9781495529 340479 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032541/WG25chr_utigTIM009_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032541/WG25chr_utigTIM009_1_merge_remdup_realign_MQ10.bam.bai +VOR004 minus ds n/a ERR5032548 PRJEB40698 SAMEA7753505 utigVOR004 ERS5500843 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/008/ERR5032548/ERR5032548.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/008/ERR5032548/ERR5032548.fastq.gz 2928198702 a5762785c04781a8e194e3a57472a54b 82956285 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032548/WG25chr_utigVOR004_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032548/WG25chr_utigVOR004_2_merge_remdup_realign_MQ10.bam.bai +MIL001 minus ds n/a ERR5032517 PRJEB40698 SAMEA7753474 utigMIL001 ERS5500812 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/007/ERR5032517/ERR5032517.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/007/ERR5032517/ERR5032517.fastq.gz 377399152 4e9048c8172e6bac76345ae85077396c 10379743 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032517/WG25chr_utigMIL001_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032517/WG25chr_utigMIL001_1_merge_remdup_realign_MQ10.bam.bai +NIK001 minus ds n/a ERR5032522 PRJEB40698 SAMEA7753479 utigNIK001 ERS5500817 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/002/ERR5032522/ERR5032522.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/002/ERR5032522/ERR5032522.fastq.gz 11676607 a6e73b6333e5ea031e1269f7fed77c06 317952 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032522/WG25chr_utigNIK001_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032522/WG25chr_utigNIK001_1_merge_remdup_realign_MQ10.bam.bai +NIK002 minus ds n/a ERR5032523 PRJEB40698 SAMEA7753480 utigNIK002 ERS5500818 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/003/ERR5032523/ERR5032523.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/003/ERR5032523/ERR5032523.fastq.gz 287294704 f077cc32bdc00be0f48f0bdd88acb3f5 7922901 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032523/WG25chr_utigNIK002_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032523/WG25chr_utigNIK002_1_merge_remdup_realign_MQ10.bam.bai +NIK003 minus ds n/a ERR5032524 PRJEB40698 SAMEA7753481 utigNIK003 ERS5500819 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/004/ERR5032524/ERR5032524.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/004/ERR5032524/ERR5032524.fastq.gz 293667603 c9b9b328f5c95b59faa41da5d8ef14fb 8282916 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032524/WG25chr_utigNIK003_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032524/WG25chr_utigNIK003_2_merge_remdup_realign_MQ10.bam.bai +NIK007 minus ds n/a ERR5032528 PRJEB40698 SAMEA7753485 utigNIK007 ERS5500823 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/008/ERR5032528/ERR5032528.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/008/ERR5032528/ERR5032528.fastq.gz 281060428 864c5a78a7ba2ac5f6ef5212bf31fe68 7641616 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032528/WG25chr_utigNIK007_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032528/WG25chr_utigNIK007_2_merge_remdup_realign_MQ10.bam.bai +RDT001 minus ds n/a ERR5032530 PRJEB40698 SAMEA7753487 utigRDT001 ERS5500825 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/000/ERR5032530/ERR5032530.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/000/ERR5032530/ERR5032530.fastq.gz 99592 1e26cfe44bf13ecb6af4c4eaea830bc2 2363 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032530/WG25chr_utigRDT001_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032530/WG25chr_utigRDT001_1_merge_remdup_realign_MQ10.bam.bai +RDT004 minus ds n/a ERR5032533 PRJEB40698 SAMEA7753490 utigRDT004 ERS5500828 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/003/ERR5032533/ERR5032533.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/003/ERR5032533/ERR5032533.fastq.gz 446553 55a299133dc70ab9c4aec503a9e2d435 11579 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032533/WG25chr_utigRDT004_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032533/WG25chr_utigRDT004_1_merge_remdup_realign_MQ10.bam.bai +SKO001 minus ds n/a ERR5032534 PRJEB40698 SAMEA7753491 utigSKO001 ERS5500829 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/004/ERR5032534/ERR5032534.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/004/ERR5032534/ERR5032534.fastq.gz 734310 dffe7bdc8f3261c000a2ffc736671bf1 20413 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032534/WG25chr_utigSKO001_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032534/WG25chr_utigSKO001_1_merge_remdup_realign_MQ10.bam.bai +TIM008 minus ds n/a ERR5032540 PRJEB40698 SAMEA7753497 utigTIM008 ERS5500835 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/000/ERR5032540/ERR5032540.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/000/ERR5032540/ERR5032540.fastq.gz 285139058 ee2a0e0e0bc4c19df42bd7122d5601d2 7946104 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032540/WG25chr_utigTIM008_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032540/WG25chr_utigTIM008_2_merge_remdup_realign_MQ10.bam.bai +VOD001 minus ds n/a ERR5032544 PRJEB40698 SAMEA7753501 utigVOD001 ERS5500839 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/004/ERR5032544/ERR5032544.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/004/ERR5032544/ERR5032544.fastq.gz 556900850 be868a530f58ff17a71f5f630063919e 15914094 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032544/WG25chr_utigVOD001_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032544/WG25chr_utigVOD001_1_merge_remdup_realign_MQ10.bam.bai +VOR002 minus ds n/a ERR5032546 PRJEB40698 SAMEA7753503 utigVOR002 ERS5500841 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/006/ERR5032546/ERR5032546.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/006/ERR5032546/ERR5032546.fastq.gz 14663578 98cc5cc2a2651a4e5c915b15957074fa 423111 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032546/WG25chr_utigVOR002_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032546/WG25chr_utigVOR002_1_merge_remdup_realign_MQ10.bam.bai +SOP002 minus ds n/a ERR5032550 PRJEB40698 SAMEA7753507 utigSOP002 ERS5500845 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/000/ERR5032550/ERR5032550.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/000/ERR5032550/ERR5032550.fastq.gz 266938619 731070b74ff5d7b5c9cff4e2b1e5f0c2 7069802 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032550/WG25chr_utigSOP002_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032550/WG25chr_utigSOP002_2_merge_remdup_realign_MQ10.bam.bai +KAR001 minus ds n/a ERR5032505 PRJEB40698 SAMEA7753462 utigKAR001 ERS5500800 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/005/ERR5032505/ERR5032505.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/005/ERR5032505/ERR5032505.fastq.gz 433435259 ad9cfdd8d0a66f9add8a8f839f487aae 12357348 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032505/WG25chr_utigKAR001_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032505/WG25chr_utigKAR001_1_merge_remdup_realign_MQ10.bam.bai +BOL003 minus ds n/a ERR5032509 PRJEB40698 SAMEA7753466 utigBOL003 ERS5500804 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/009/ERR5032509/ERR5032509.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/009/ERR5032509/ERR5032509.fastq.gz 2512568035 89cff6107edee9fb46cf56bdc2d8dbf9 73526006 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032509/WG25chr_utigBOL003_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032509/WG25chr_utigBOL003_2_merge_remdup_realign_MQ10.bam.bai +GOL001 minus ds n/a ERR5032510 PRJEB40698 SAMEA7753467 utigGOL001 ERS5500805 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/000/ERR5032510/ERR5032510.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/000/ERR5032510/ERR5032510.fastq.gz 273791207 79c3f8071d70fad6b6c64e7384de1344 7518746 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032510/WG25chr_utigGOL001_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032510/WG25chr_utigGOL001_2_merge_remdup_realign_MQ10.bam.bai +MOT001 minus ds n/a ERR5032519 PRJEB40698 SAMEA7753476 utigMOT001 ERS5500814 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/009/ERR5032519/ERR5032519.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/009/ERR5032519/ERR5032519.fastq.gz 19358370 51c6b3cb3ae5155042a217773c540974 569158 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032519/WG25chr_utigMOT001_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032519/WG25chr_utigMOT001_1_merge_remdup_realign_MQ10.bam.bai +NIK004 minus ds n/a ERR5032525 PRJEB40698 SAMEA7753482 utigNIK004 ERS5500820 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/005/ERR5032525/ERR5032525.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/005/ERR5032525/ERR5032525.fastq.gz 415986784 d072fda2465875f59117eef91dbd8750 11132329 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032525/WG25chr_utigNIK004_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032525/WG25chr_utigNIK004_1_merge_remdup_realign_MQ10.bam.bai +NIK005 minus ds n/a ERR5032526 PRJEB40698 SAMEA7753483 utigNIK005 ERS5500821 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/006/ERR5032526/ERR5032526.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/006/ERR5032526/ERR5032526.fastq.gz 302284846 aa8e1b351024c523d80bba74109ab0bf 9088525 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032526/WG25chr_utigNIK005_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032526/WG25chr_utigNIK005_2_merge_remdup_realign_MQ10.bam.bai +NIK006 minus ds n/a ERR5032527 PRJEB40698 SAMEA7753484 utigNIK006 ERS5500822 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/007/ERR5032527/ERR5032527.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/007/ERR5032527/ERR5032527.fastq.gz 11767118 81f963ada7fcd86de4a95cd6a4b554a2 323056 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032527/WG25chr_utigNIK006_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032527/WG25chr_utigNIK006_1_merge_remdup_realign_MQ10.bam.bai +NIK008AB minus ds n/a ERR5032529 PRJEB40698 SAMEA7753486 utigNIK008AB ERS5500824 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/009/ERR5032529/ERR5032529.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/009/ERR5032529/ERR5032529.fastq.gz 2897366105 ff14beb60a1074423bde4d3a12b8ccfe 79023895 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032529/WG25chr_utigNIK008AB_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032529/WG25chr_utigNIK008AB_2_merge_remdup_realign_MQ10.bam.bai +RDT003 minus ds n/a ERR5032532 PRJEB40698 SAMEA7753489 utigRDT003 ERS5500827 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/002/ERR5032532/ERR5032532.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/002/ERR5032532/ERR5032532.fastq.gz 1501696 cd1776a521a4e2b75810e345fd4902aa 39580 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032532/WG25chr_utigRDT003_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032532/WG25chr_utigRDT003_1_merge_remdup_realign_MQ10.bam.bai +TIM001 minus ds n/a ERR5032535 PRJEB40698 SAMEA7753492 utigTIM001 ERS5500830 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/005/ERR5032535/ERR5032535.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/005/ERR5032535/ERR5032535.fastq.gz 43336875 5bd2b4ffc2152e211c1a97fe56c7d419 1195505 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032535/WG25chr_utigTIM001_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032535/WG25chr_utigTIM001_1_merge_remdup_realign_MQ10.bam.bai +TIM002 minus ds n/a ERR5032536 PRJEB40698 SAMEA7753493 utigTIM002 ERS5500831 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/006/ERR5032536/ERR5032536.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/006/ERR5032536/ERR5032536.fastq.gz 3645788 429fc2446175d093a1db2bcaa38d6a22 100097 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032536/WG25chr_utigTIM002_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032536/WG25chr_utigTIM002_1_merge_remdup_realign_MQ10.bam.bai +TIM003 minus ds n/a ERR5032537 PRJEB40698 SAMEA7753494 utigTIM003 ERS5500832 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/007/ERR5032537/ERR5032537.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/007/ERR5032537/ERR5032537.fastq.gz 12089978 7c207faa7c54489b8aa76d1848b82366 343078 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032537/WG25chr_utigTIM003_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032537/WG25chr_utigTIM003_1_merge_remdup_realign_MQ10.bam.bai +TIM005 minus ds n/a ERR5032538 PRJEB40698 SAMEA7753495 utigTIM005 ERS5500833 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/008/ERR5032538/ERR5032538.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/008/ERR5032538/ERR5032538.fastq.gz 18018418 2b656eb2e9816b7b20d2d11270b380c3 515817 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032538/WG25chr_utigTIM005_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032538/WG25chr_utigTIM005_1_merge_remdup_realign_MQ10.bam.bai +TIM006 minus ds n/a ERR5032539 PRJEB40698 SAMEA7753496 utigTIM006 ERS5500834 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/009/ERR5032539/ERR5032539.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/009/ERR5032539/ERR5032539.fastq.gz 279572298 a9c24a0b293395093070159942b1ed00 7826327 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032539/WG25chr_utigTIM006_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032539/WG25chr_utigTIM006_2_merge_remdup_realign_MQ10.bam.bai +TIM010 minus ds n/a ERR5032542 PRJEB40698 SAMEA7753499 utigTIM010 ERS5500837 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/002/ERR5032542/ERR5032542.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/002/ERR5032542/ERR5032542.fastq.gz 19433612 d3691f8629e009e85d801fff1d03c314 591570 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032542/WG25chr_utigTIM010_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032542/WG25chr_utigTIM010_1_merge_remdup_realign_MQ10.bam.bai +TIM011 minus ds n/a ERR5032543 PRJEB40698 SAMEA7753500 utigTIM011 ERS5500838 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/003/ERR5032543/ERR5032543.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/003/ERR5032543/ERR5032543.fastq.gz 14584229 aace582e237c07717356fec190836226 428145 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032543/WG25chr_utigTIM011_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032543/WG25chr_utigTIM011_1_merge_remdup_realign_MQ10.bam.bai +VOR001 minus ds n/a ERR5032545 PRJEB40698 SAMEA7753502 utigVOR001 ERS5500840 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/005/ERR5032545/ERR5032545.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/005/ERR5032545/ERR5032545.fastq.gz 9005717 97cb93e36360b03007f59f3c2f6ee017 250420 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032545/WG25chr_utigVOR001_1_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032545/WG25chr_utigVOR001_1_merge_remdup_realign_MQ10.bam.bai +VOR003 minus ds n/a ERR5032547 PRJEB40698 SAMEA7753504 utigVOR003 ERS5500842 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/007/ERR5032547/ERR5032547.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/007/ERR5032547/ERR5032547.fastq.gz 273415721 bd6924fbf56042850967c27de05d2bae 7308743 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032547/WG25chr_utigVOR003_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032547/WG25chr_utigVOR003_2_merge_remdup_realign_MQ10.bam.bai +VOR005 minus ds n/a ERR5032549 PRJEB40698 SAMEA7753506 utigVOR005 ERS5500844 2021-01-19 2020-12-28 NextSeq 500 SINGLE METAGENOMIC ILLUMINA unspecified WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR503/009/ERR5032549/ERR5032549.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR503/009/ERR5032549/ERR5032549.fastq.gz 271157407 522a9e209272080ca7aa15b94b3557ee 7417758 ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032549/WG25chr_utigVOR005_2_merge_remdup_realign_MQ10.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR503/ERR5032549/WG25chr_utigVOR005_2_merge_remdup_realign_MQ10.bam.bai From f57d7200318b23714d725075e9c02fce3607f3e2 Mon Sep 17 00:00:00 2001 From: delphis-bot Date: Tue, 25 Jul 2023 13:12:33 +0000 Subject: [PATCH 2/6] [automated] Create processing backbone from SSF files --- .../2021_Saag_EastEuropean.config | 39 +++++++++++++++ .../2021_Saag_EastEuropean.tsv | 48 +++++++++++++++++++ .../2021_Saag_EastEuropean.tsv_patch.sh | 45 +++++++++++++++++ .../script_versions.txt | 2 + 4 files changed, 134 insertions(+) create mode 100644 packages/2021_Saag_EastEuropean/2021_Saag_EastEuropean.config create mode 100644 packages/2021_Saag_EastEuropean/2021_Saag_EastEuropean.tsv create mode 100755 packages/2021_Saag_EastEuropean/2021_Saag_EastEuropean.tsv_patch.sh create mode 100644 packages/2021_Saag_EastEuropean/script_versions.txt diff --git a/packages/2021_Saag_EastEuropean/2021_Saag_EastEuropean.config b/packages/2021_Saag_EastEuropean/2021_Saag_EastEuropean.config new file mode 100644 index 0000000..1b03016 --- /dev/null +++ b/packages/2021_Saag_EastEuropean/2021_Saag_EastEuropean.config @@ -0,0 +1,39 @@ +// Keep track of config versions +config_template_version='0.2.0dev' +package_config_version='0.2.0dev' + +// This configuration file is designed to be a used with the nf-core/eager pipeline. +// Instead of having to specify all other configurations for the Minotaur pipeline +// on runtime, they are all contained in this file and loaded automatically upon +// specifying this config file during runtime. Additionally, any parameters that +// need to be altered from the defaults can be specified here. +// +// The intention is to make it easy for users to understand and reproduce the output +// from processing with the Minotaur workflow processing from the contents of a +// single file. + +// Load configuration profiles +includeConfig "../../conf/EVA_cluster.config" // Cluster-specific configurations for nf-core/eager execution at MPI-EVA +includeConfig "../../conf/Minotaur.config" // Default nf-core/eager parameters for Minotaur processing. + +// The following config file specifies BED files for on-target endogenous DNA calculation and mean coverage as well as pseudohaploid genotyping. +// TODO: Select the appropriate config for the CaptureType of the package. +includeConfig '../../conf/CaptureType_profiles/1240K.config' + +params { + // Keep track of config file versions used when processing + config_profile_description = "${config_profile_description}\nconfig_template_version: ${config_template_version}\npackage_config_version: ${package_config_version}" + config_profile_contact = "Thiseas C. Lamnidis (@TCLamnidis)" + + /* + TODO: If you need to change any of the default processing parameters for this package + you can specify these parameters below. + Any parameters not specified in any of the config files default to their nf-core/eager default values. + + For information on all available parameters and their default values see: + https://nf-co.re/eager/2.4.6/parameters + + You can see the default values for parameters within poseidon-eager at: + https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Minotaur.config + */ +} diff --git a/packages/2021_Saag_EastEuropean/2021_Saag_EastEuropean.tsv b/packages/2021_Saag_EastEuropean/2021_Saag_EastEuropean.tsv new file mode 100644 index 0000000..70a9f30 --- /dev/null +++ b/packages/2021_Saag_EastEuropean/2021_Saag_EastEuropean.tsv @@ -0,0 +1,48 @@ +Sample_Name Library_ID Lane Colour_Chemistry SeqType Organism Strandedness UDG_Treatment R1 R2 BAM R1_target_file R2_target_file +BER001 BER001_unspecified 1 4 SE Homo sapiens (modern human) double none /BER001_unspecified_L1_R1.fastq.gz NA NA ERR5032504.fastq.gz NA +PES001 PES001_unspecified 1 4 SE Homo sapiens (modern human) double none /PES001_unspecified_L1_R1.fastq.gz NA NA ERR5032506.fastq.gz NA +BOL001 BOL001_unspecified 1 4 SE Homo sapiens (modern human) double none /BOL001_unspecified_L1_R1.fastq.gz NA NA ERR5032507.fastq.gz NA +HAN001 HAN001_unspecified 1 4 SE Homo sapiens (modern human) double none /HAN001_unspecified_L1_R1.fastq.gz NA NA ERR5032512.fastq.gz NA +HAN003 HAN003_unspecified 1 4 SE Homo sapiens (modern human) double none /HAN003_unspecified_L1_R1.fastq.gz NA NA ERR5032514.fastq.gz NA +BOL002 BOL002_unspecified 1 4 SE Homo sapiens (modern human) double none /BOL002_unspecified_L1_R1.fastq.gz NA NA ERR5032508.fastq.gz NA +IVA001 IVA001_unspecified 1 4 SE Homo sapiens (modern human) double none /IVA001_unspecified_L1_R1.fastq.gz NA NA ERR5032516.fastq.gz NA +HAL001 HAL001_unspecified 1 4 SE Homo sapiens (modern human) double none /HAL001_unspecified_L1_R1.fastq.gz NA NA ERR5032511.fastq.gz NA +HAN002 HAN002_unspecified 1 4 SE Homo sapiens (modern human) double none /HAN002_unspecified_L1_R1.fastq.gz NA NA ERR5032513.fastq.gz NA +MIL002 MIL002_unspecified 1 4 SE Homo sapiens (modern human) double none /MIL002_unspecified_L1_R1.fastq.gz NA NA ERR5032518.fastq.gz NA +NAU001 NAU001_unspecified 1 4 SE Homo sapiens (modern human) double none /NAU001_unspecified_L1_R1.fastq.gz NA NA ERR5032520.fastq.gz NA +NAU002 NAU002_unspecified 1 4 SE Homo sapiens (modern human) double none /NAU002_unspecified_L1_R1.fastq.gz NA NA ERR5032521.fastq.gz NA +HAN004 HAN004_unspecified 1 4 SE Homo sapiens (modern human) double none /HAN004_unspecified_L1_R1.fastq.gz NA NA ERR5032515.fastq.gz NA +RDT002 RDT002_unspecified 1 4 SE Homo sapiens (modern human) double none /RDT002_unspecified_L1_R1.fastq.gz NA NA ERR5032531.fastq.gz NA +TIM009 TIM009_unspecified 1 4 SE Homo sapiens (modern human) double none /TIM009_unspecified_L1_R1.fastq.gz NA NA ERR5032541.fastq.gz NA +VOR004 VOR004_unspecified 1 4 SE Homo sapiens (modern human) double none /VOR004_unspecified_L1_R1.fastq.gz NA NA ERR5032548.fastq.gz NA +MIL001 MIL001_unspecified 1 4 SE Homo sapiens (modern human) double none /MIL001_unspecified_L1_R1.fastq.gz NA NA ERR5032517.fastq.gz NA +NIK001 NIK001_unspecified 1 4 SE Homo sapiens (modern human) double none /NIK001_unspecified_L1_R1.fastq.gz NA NA ERR5032522.fastq.gz NA +NIK002 NIK002_unspecified 1 4 SE Homo sapiens (modern human) double none /NIK002_unspecified_L1_R1.fastq.gz NA NA ERR5032523.fastq.gz NA +NIK003 NIK003_unspecified 1 4 SE Homo sapiens (modern human) double none /NIK003_unspecified_L1_R1.fastq.gz NA NA ERR5032524.fastq.gz NA +NIK007 NIK007_unspecified 1 4 SE Homo sapiens (modern human) double none /NIK007_unspecified_L1_R1.fastq.gz NA NA ERR5032528.fastq.gz NA +RDT001 RDT001_unspecified 1 4 SE Homo sapiens (modern human) double none /RDT001_unspecified_L1_R1.fastq.gz NA NA ERR5032530.fastq.gz NA +RDT004 RDT004_unspecified 1 4 SE Homo sapiens (modern human) double none /RDT004_unspecified_L1_R1.fastq.gz NA NA ERR5032533.fastq.gz NA +SKO001 SKO001_unspecified 1 4 SE Homo sapiens (modern human) double none /SKO001_unspecified_L1_R1.fastq.gz NA NA ERR5032534.fastq.gz NA +TIM008 TIM008_unspecified 1 4 SE Homo sapiens (modern human) double none /TIM008_unspecified_L1_R1.fastq.gz NA NA ERR5032540.fastq.gz NA +VOD001 VOD001_unspecified 1 4 SE Homo sapiens (modern human) double none /VOD001_unspecified_L1_R1.fastq.gz NA NA ERR5032544.fastq.gz NA +VOR002 VOR002_unspecified 1 4 SE Homo sapiens (modern human) double none /VOR002_unspecified_L1_R1.fastq.gz NA NA ERR5032546.fastq.gz NA +SOP002 SOP002_unspecified 1 4 SE Homo sapiens (modern human) double none /SOP002_unspecified_L1_R1.fastq.gz NA NA ERR5032550.fastq.gz NA +KAR001 KAR001_unspecified 1 4 SE Homo sapiens (modern human) double none /KAR001_unspecified_L1_R1.fastq.gz NA NA ERR5032505.fastq.gz NA +BOL003 BOL003_unspecified 1 4 SE Homo sapiens (modern human) double none /BOL003_unspecified_L1_R1.fastq.gz NA NA ERR5032509.fastq.gz NA +GOL001 GOL001_unspecified 1 4 SE Homo sapiens (modern human) double none /GOL001_unspecified_L1_R1.fastq.gz NA NA ERR5032510.fastq.gz NA +MOT001 MOT001_unspecified 1 4 SE Homo sapiens (modern human) double none /MOT001_unspecified_L1_R1.fastq.gz NA NA ERR5032519.fastq.gz NA +NIK004 NIK004_unspecified 1 4 SE Homo sapiens (modern human) double none /NIK004_unspecified_L1_R1.fastq.gz NA NA ERR5032525.fastq.gz NA +NIK005 NIK005_unspecified 1 4 SE Homo sapiens (modern human) double none /NIK005_unspecified_L1_R1.fastq.gz NA NA ERR5032526.fastq.gz NA +NIK006 NIK006_unspecified 1 4 SE Homo sapiens (modern human) double none /NIK006_unspecified_L1_R1.fastq.gz NA NA ERR5032527.fastq.gz NA +NIK008AB NIK008AB_unspecified 1 4 SE Homo sapiens (modern human) double none /NIK008AB_unspecified_L1_R1.fastq.gz NA NA ERR5032529.fastq.gz NA +RDT003 RDT003_unspecified 1 4 SE Homo sapiens (modern human) double none /RDT003_unspecified_L1_R1.fastq.gz NA NA ERR5032532.fastq.gz NA +TIM001 TIM001_unspecified 1 4 SE Homo sapiens (modern human) double none /TIM001_unspecified_L1_R1.fastq.gz NA NA ERR5032535.fastq.gz NA +TIM002 TIM002_unspecified 1 4 SE Homo sapiens (modern human) double none /TIM002_unspecified_L1_R1.fastq.gz NA NA ERR5032536.fastq.gz NA +TIM003 TIM003_unspecified 1 4 SE Homo sapiens (modern human) double none /TIM003_unspecified_L1_R1.fastq.gz NA NA ERR5032537.fastq.gz NA +TIM005 TIM005_unspecified 1 4 SE Homo sapiens (modern human) double none /TIM005_unspecified_L1_R1.fastq.gz NA NA ERR5032538.fastq.gz NA +TIM006 TIM006_unspecified 1 4 SE Homo sapiens (modern human) double none /TIM006_unspecified_L1_R1.fastq.gz NA NA ERR5032539.fastq.gz NA +TIM010 TIM010_unspecified 1 4 SE Homo sapiens (modern human) double none /TIM010_unspecified_L1_R1.fastq.gz NA NA ERR5032542.fastq.gz NA +TIM011 TIM011_unspecified 1 4 SE Homo sapiens (modern human) double none /TIM011_unspecified_L1_R1.fastq.gz NA NA ERR5032543.fastq.gz NA +VOR001 VOR001_unspecified 1 4 SE Homo sapiens (modern human) double none /VOR001_unspecified_L1_R1.fastq.gz NA NA ERR5032545.fastq.gz NA +VOR003 VOR003_unspecified 1 4 SE Homo sapiens (modern human) double none /VOR003_unspecified_L1_R1.fastq.gz NA NA ERR5032547.fastq.gz NA +VOR005 VOR005_unspecified 1 4 SE Homo sapiens (modern human) double none /VOR005_unspecified_L1_R1.fastq.gz NA NA ERR5032549.fastq.gz NA diff --git a/packages/2021_Saag_EastEuropean/2021_Saag_EastEuropean.tsv_patch.sh b/packages/2021_Saag_EastEuropean/2021_Saag_EastEuropean.tsv_patch.sh new file mode 100755 index 0000000..422e836 --- /dev/null +++ b/packages/2021_Saag_EastEuropean/2021_Saag_EastEuropean.tsv_patch.sh @@ -0,0 +1,45 @@ +#!/usr/bin/env bash +set -uo pipefail ## Pipefail, complain on new unassigned variables. + +## Track the version of the TSV_patch template used +VERSION='0.2.0dev' + +## This script is applied to the eager input TSV file locally to edit the dummy +## path to the fastQ files added by `create_eager_input.sh` to a real local +## path provided as a positional argument. Any further local tweaks to the +## TSV before running eager should be added below that in the form of bash +## commands to aid in reproducibility. + +## usage tsv_patch.sh + +local_data_dir="$(readlink -f ${1})" +input_tsv="$(readlink -f ${2})" +output_tsv="$(dirname ${local_data_dir})/$(basename -s ".tsv" ${input_tsv}).finalised.tsv" +columns_to_keep=("Sample_Name" "Library_ID" "Lane" "Colour_Chemistry" "SeqType" "Organism" "Strandedness" "UDG_Treatment" "R1" "R2" "BAM") +source $(dirname ${2})/../../scripts/source_me.sh ## Load helper functions + +## Index non-proliferated columns and exclude them from the finalised TSV +cut_selector='' +tsv_header=($(head -n1 ${input_tsv})) +for col_name in ${columns_to_keep[@]}; do + let idx=$(get_index_of ${col_name} "${columns_to_keep[@]}")+1 ## awk uses 1-based indexing + if [[ ! ${idx} -eq -1 ]]; then + cut_selector+="${idx}," + fi +done + +## Remove added columns, and put columns in right order +cut -f ${cut_selector%,} ${input_tsv} > ${output_tsv} +sed -i -e "s||${local_data_dir}|g" ${output_tsv} + +## Any further commands to edit the file before finalisation should be added below as shown +# sed -ie 's/replace_this/with_this/g' ${output_tsv} + +## Keep track of versions +version_file="$(dirname ${input_tsv})/script_versions.txt" +## Remove versions from older run if there +grep -v -F -e "$(basename ${0})" -e "source_me.sh for final TSV" ${version_file} >${version_file}.new +## Then add new versions +echo -e "$(basename ${0}):\t${VERSION}" >> ${version_file}.new +echo -e "source_me.sh for final TSV:\t${HELPER_FUNCTION_VERSION}" >>${version_file}.new +mv ${version_file}.new ${version_file} diff --git a/packages/2021_Saag_EastEuropean/script_versions.txt b/packages/2021_Saag_EastEuropean/script_versions.txt new file mode 100644 index 0000000..be6857b --- /dev/null +++ b/packages/2021_Saag_EastEuropean/script_versions.txt @@ -0,0 +1,2 @@ +create_eager_input.sh: 0.2.1dev +source_me.sh for initial TSV: 0.2.1dev From 1cc9912b36a95d2c019d72f78a910b94d710a8da Mon Sep 17 00:00:00 2001 From: Thiseas Christos Lamnidis Date: Tue, 25 Jul 2023 15:47:08 +0200 Subject: [PATCH 3/6] Add 2020_Nagele_Carribbean ssf --- .../2020_Nagele_Caribbean.ssf | 185 ++++++++++++++++++ 1 file changed, 185 insertions(+) create mode 100644 packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.ssf diff --git a/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.ssf b/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.ssf new file mode 100644 index 0000000..b8becd1 --- /dev/null +++ b/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.ssf @@ -0,0 +1,185 @@ +poseidon_IDs udg library_built notes run_accession study_accession sample_accession sample_alias secondary_sample_accession first_public last_updated instrument_model library_layout library_source instrument_platform library_name library_strategy fastq_ftp fastq_aspera fastq_bytes fastq_md5 read_count submitted_ftp +ALG002 minus ds n/a ERR4170303 PRJEB37518 SAMEA6850808 ALG002 ERS4578402 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA ALG002.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170303/ERR4170303.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170303/ERR4170303.fastq.gz 66991543 27128ba3ec0a9bcc6a79264202433701 1850516 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170303/ALG002.A0101.TF1.12.bam +ALG003 minus ds n/a ERR4170304 PRJEB37518 SAMEA6850809 ALG003 ERS4578403 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA ALG003.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170304/ERR4170304.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170304/ERR4170304.fastq.gz 65702073 f985dc48df94706734ab54f59e4c051a 1818962 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170304/ALG003.A0101.TF1.12.bam +CAO002008 half ds n/a ERR4170309 PRJEB37518 SAMEA6850814 CAO002008 ERS4578408 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO002008.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/009/ERR4170309/ERR4170309.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/009/ERR4170309/ERR4170309.fastq.gz 156014279 8012b89a98b4f7172f748e829331acda 4091385 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170309/CAO002008.TF1.1.bam +CAO006 half ds n/a ERR4170311 PRJEB37518 SAMEA6850816 CAO006 ERS4578410 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO006.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/001/ERR4170311/ERR4170311.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/001/ERR4170311/ERR4170311.fastq.gz 13003317 d0a6750bea4107d8ed339616a9aa185d 323322 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170311/CAO006.A0101.TF1.1.bam +CAO007 half ds n/a ERR4170312 PRJEB37518 SAMEA6850817 CAO007 ERS4578411 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO007.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170312/ERR4170312.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170312/ERR4170312.fastq.gz 108667005 dae747c1d5c638b9cd0015c0565cd82e 2786042 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170312/CAO007.A0101.TF1.1.bam +CAO012 half ds n/a ERR4170316 PRJEB37518 SAMEA6850821 CAO012 ERS4578415 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO012.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170316/ERR4170316.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170316/ERR4170316.fastq.gz 247343594 2a9863c9b53feb3f13d932d088e8f553 7027230 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170316/CAO012.A0101.TF1.1.bam +CAO015 half ds n/a ERR4170318 PRJEB37518 SAMEA6850823 CAO015 ERS4578417 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO015.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/008/ERR4170318/ERR4170318.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/008/ERR4170318/ERR4170318.fastq.gz 251226593 c22600acf2da64250e234d3fbdcc5e15 8017370 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170318/CAO015.A0101.TF1.1.bam +CAO022026 half ds n/a ERR4170325 PRJEB37518 SAMEA6850830 CAO022026 ERS4578424 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO022026.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170325/ERR4170325.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170325/ERR4170325.fastq.gz 616983466 e3a367971649131fb4154aa577d1c984 18564421 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170325/CAO022026.TF1.1.bam +CAO027 half ds n/a ERR4170328 PRJEB37518 SAMEA6850833 CAO027 ERS4578427 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO027.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/008/ERR4170328/ERR4170328.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/008/ERR4170328/ERR4170328.fastq.gz 283399824 1d761412a2cb71e94008443d19067517 8215403 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170328/CAO027.A0101.TF1.1.bam +CAO030 half ds n/a ERR4170331 PRJEB37518 SAMEA6850836 CAO030 ERS4578430 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO030.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/001/ERR4170331/ERR4170331.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/001/ERR4170331/ERR4170331.fastq.gz 148645297 d1fd08bf87a2147b9886e66acb84ac6c 4425173 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170331/CAO030.A0101.TF1.1.bam +CAO031 half ds n/a ERR4170332 PRJEB37518 SAMEA6850837 CAO031 ERS4578431 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO031.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170332/ERR4170332.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170332/ERR4170332.fastq.gz 225189168 3f35b1ff99ae882696f6423a37ceb4bb 6616975 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170332/CAO031.A0101.TF1.1.bam +CDE001 half ds n/a ERR4170334 PRJEB37518 SAMEA6850839 CDE001 ERS4578433 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CDE001.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170334/ERR4170334.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170334/ERR4170334.fastq.gz 343272523 36d8cba012946e4c1bd9d82e08b0437b 9760868 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170334/CDE001.A0101.TF1.1.bam +CDE005 half ds n/a ERR4170338 PRJEB37518 SAMEA6850843 CDE005 ERS4578437 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CDE005.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/008/ERR4170338/ERR4170338.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/008/ERR4170338/ERR4170338.fastq.gz 350109556 98f63e3369666fb83e2ec0036e1a6b95 10433418 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170338/CDE005.A0101.TF1.1.bam +CIP001 half ds n/a ERR4170339 PRJEB37518 SAMEA6850844 CIP001 ERS4578438 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CIP001.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/009/ERR4170339/ERR4170339.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/009/ERR4170339/ERR4170339.fastq.gz 81115641 7265cf17fb7270e880aa4c28253bbf94 2182967 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170339/CIP001.A0101.TF1.12.bam +CIP003 half ds n/a ERR4170341 PRJEB37518 SAMEA6850846 CIP003 ERS4578440 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CIP003.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/001/ERR4170341/ERR4170341.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/001/ERR4170341/ERR4170341.fastq.gz 117370841 1af8432f88983d670ef3af5583946f83 3256981 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170341/CIP003.A0101.TF1.12.bam +CIP008 half ds n/a ERR4170343 PRJEB37518 SAMEA6850848 CIP008 ERS4578442 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CIP008.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170343/ERR4170343.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170343/ERR4170343.fastq.gz 46697082 197011805cb6efcddb54a797ead6e045 1282164 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170343/CIP008.A0101.TF1.12.bam +CIP009 half ds n/a ERR4170344 PRJEB37518 SAMEA6850849 CIP009 ERS4578443 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CIP009.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170344/ERR4170344.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170344/ERR4170344.fastq.gz 28084914 4dec669c28562fd95d87493d6af6d663 772400 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170344/CIP009.A0101.TF1.12.bam +CIP011 half ds n/a ERR4170346 PRJEB37518 SAMEA6850851 CIP011 ERS4578445 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CIP011.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170346/ERR4170346.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170346/ERR4170346.fastq.gz 43035812 4a2958985ab17d7bd75c4d79c79a39f3 1175131 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170346/CIP011.A0101.TF1.12.bam +ELM001 half ds n/a ERR4170351 PRJEB37518 SAMEA6850856 ELM001 ERS4578450 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA ELM001.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/001/ERR4170351/ERR4170351.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/001/ERR4170351/ERR4170351.fastq.gz 196098288 f55fbec6a3c0d4f2b9ee01f6b8bf0d9f 5268923 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170351/ELM001.A0101.TF1.1.bam +GUY002 half ds n/a ERR4170353 PRJEB37518 SAMEA6850858 GUY002 ERS4578452 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUY002.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170353/ERR4170353.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170353/ERR4170353.fastq.gz 163604922 d2a700582d4403b8e71bc60ddcc1d5d6 5018179 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170353/GUY002.A0101.TF1.1.bam +LAV006 half ds n/a ERR4170360 PRJEB37518 SAMEA6850865 LAV006 ERS4578459 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV006.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/000/ERR4170360/ERR4170360.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/000/ERR4170360/ERR4170360.fastq.gz 122449947 acff1dd14bd87c7f5f34dd9c6971e5bf 3539031 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170360/LAV006.A0101.TF1.12.bam +PCA002 half ds n/a ERR4170370 PRJEB37518 SAMEA6850875 PCA002 ERS4578469 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PCA002.A0101.TF1.1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/000/ERR4170370/ERR4170370.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/000/ERR4170370/ERR4170370.fastq.gz 77768616 eec98dd074536de3e1ffd8c9c6cd1855 2236148 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170370/PCA002.A0101.TF1.12.bam +PCA009 half ds n/a ERR4170372 PRJEB37518 SAMEA6850877 PCA009 ERS4578471 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PCA009.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170372/ERR4170372.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170372/ERR4170372.fastq.gz 26673158 d2d5870ca049a867de2b2cd3fd0a45a1 781339 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170372/PCA009.A0101.TF1.1.bam +PDI003 half ds n/a ERR4170378 PRJEB37518 SAMEA6850883 PDI003 ERS4578477 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDI003.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/008/ERR4170378/ERR4170378.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/008/ERR4170378/ERR4170378.fastq.gz 18274135 46238095d0a564072798682647644a03 521033 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170378/PDI003.A0101.TF1.1.bam +PDI010 half ds n/a ERR4170382 PRJEB37518 SAMEA6850887 PDI010 ERS4578481 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDI010.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170382/ERR4170382.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170382/ERR4170382.fastq.gz 151881583 51124702abed9c156cfca4081d5f8b50 4699571 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170382/PDI010.A0101.TF1.1.bam +PDI011 half ds n/a ERR4170383 PRJEB37518 SAMEA6850888 PDI011 ERS4578482 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDI011.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170383/ERR4170383.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170383/ERR4170383.fastq.gz 125640347 66e950fd5f91713ac1977931d685aa7b 3663357 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170383/PDI011.A0101.TF1.1.bam +PDM001 half ds n/a ERR4170385 PRJEB37518 SAMEA6850890 PDM001 ERS4578484 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDM001.A0101.TF12.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170385/ERR4170385.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170385/ERR4170385.fastq.gz 48655519 573e5c02ff9f64cec5adc8c6222e2bf9 1582683 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170385/PDM001.A0101.TF1.12.bam +PDM002 half ds n/a ERR4170386 PRJEB37518 SAMEA6850891 PDM002 ERS4578485 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDM002.A0101.TF12.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170386/ERR4170386.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170386/ERR4170386.fastq.gz 35699690 69e9c8b219168594b7d7d21c242cf0b0 1157233 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170386/PDM002.A0101.TF1.12.bam +PDM008 half ds n/a ERR4170390 PRJEB37518 SAMEA6850895 PDM008 ERS4578489 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDM008.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/000/ERR4170390/ERR4170390.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/000/ERR4170390/ERR4170390.fastq.gz 51439221 71a9bb68e0ca25a4512edc9a2fd40cd0 1565608 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170390/PDM008.A0101.TF1.1.bam +TIB002 half ds n/a ERR4170394 PRJEB37518 SAMEA6850899 TIB002 ERS4578493 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA TIB002.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170394/ERR4170394.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170394/ERR4170394.fastq.gz 32366404 3eda0e61879297cc9f5dc3bf4f6ba802 891849 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170394/TIB002.A0101.TF1.1.bam +ALG002 minus ds n/a ERR4170396 PRJEB37518 SAMEA6850808 ALG002 ERS4578402 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA ALG002.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170396/ERR4170396.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170396/ERR4170396.fastq.gz 953101 47132501060ba4be12772e48a4048cb2 61811 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170396/ALG002.A0101.MT1.1.bam +CAO001 half ds n/a ERR4170401 PRJEB37518 SAMEA6850813 CAO001 ERS4578407 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO001.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/001/ERR4170401/ERR4170401.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/001/ERR4170401/ERR4170401.fastq.gz 1120994 91da0930d9d6b3f256a206fbca7ae96e 80498 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170401/CAO001.A0101.MT1.1.bam +CAO002008 half ds n/a ERR4170402 PRJEB37518 SAMEA6850814 CAO002008 ERS4578408 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO002008.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170402/ERR4170402.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170402/ERR4170402.fastq.gz 433857 f66b40b81e783705cfeed1c765a8b3b6 29897 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170402/CAO002008.A0101.MT1.1.bam +CAO007 half ds n/a ERR4170405 PRJEB37518 SAMEA6850817 CAO007 ERS4578411 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO007.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170405/ERR4170405.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170405/ERR4170405.fastq.gz 127864 93da6856a2a068b46604b9c242a6c9a5 7403 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170405/CAO007.A0101.MT1.1.bam +CAO010 half ds n/a ERR4170407 PRJEB37518 SAMEA6850819 CAO010 ERS4578413 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO010.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/007/ERR4170407/ERR4170407.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/007/ERR4170407/ERR4170407.fastq.gz 181100 35dff71ba570086224154b3d84192333 11434 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170407/CAO010.A0101.MT1.1.bam +CAO015 half ds n/a ERR4170411 PRJEB37518 SAMEA6850823 CAO015 ERS4578417 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO015.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/001/ERR4170411/ERR4170411.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/001/ERR4170411/ERR4170411.fastq.gz 360345 daf2f2219dcd2a4ba40ce3355c685075 24242 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170411/CAO015.A0101.MT1.1.bam +CAO019 half ds n/a ERR4170415 PRJEB37518 SAMEA6850827 CAO019 ERS4578421 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO019.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170415/ERR4170415.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170415/ERR4170415.fastq.gz 92923 e33670342753500be79ad4f675b0424e 6022 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170415/CAO019.A0101.MT1.1.bam +CAO021 half ds n/a ERR4170417 PRJEB37518 SAMEA6850829 CAO021 ERS4578423 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO021.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/007/ERR4170417/ERR4170417.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/007/ERR4170417/ERR4170417.fastq.gz 465288 f0eb86952661f13f15dc877ede7fcd52 32533 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170417/CAO021.A0101.MT1.1.bam +CAO024 half ds n/a ERR4170420 PRJEB37518 SAMEA6850832 CAO024 ERS4578426 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO024.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/000/ERR4170420/ERR4170420.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/000/ERR4170420/ERR4170420.fastq.gz 464383 78d01c2a925a7022d22e9302d383ebca 32290 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170420/CAO024.A0101.MT1.1.bam +CAO029 half ds n/a ERR4170423 PRJEB37518 SAMEA6850835 CAO029 ERS4578429 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO029.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170423/ERR4170423.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170423/ERR4170423.fastq.gz 451517 fd50f704b953471c5f82e1237a0ad342 32573 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170423/CAO029.A0101.MT1.1.bam +CAO031 half ds n/a ERR4170425 PRJEB37518 SAMEA6850837 CAO031 ERS4578431 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO031.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170425/ERR4170425.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170425/ERR4170425.fastq.gz 411439 6b1ca32aa5686662d4deb34600ba03bf 26881 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170425/CAO031.A0101.MT1.1.bam +CIP002 half ds n/a ERR4170433 PRJEB37518 SAMEA6850845 CIP002 ERS4578439 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CIP002.A0101.MT1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170433/ERR4170433.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170433/ERR4170433.fastq.gz 295461 e4e708384d818375d40bdf2a731238a3 12863 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170433/CIP002.A0101.MT1.12.bam +CIP003 half ds n/a ERR4170434 PRJEB37518 SAMEA6850846 CIP003 ERS4578440 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CIP003.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170434/ERR4170434.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170434/ERR4170434.fastq.gz 934192 6bc18f0dbcef241cd4ff153763703819 60582 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170434/CIP003.A0101.MT1.1.bam +CIP007012 half ds n/a ERR4170435 PRJEB37518 SAMEA6850847 CIP007012 ERS4578441 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CIP007012.A0101.MT1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170435/ERR4170435.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170435/ERR4170435.fastq.gz 718295 155118284175bfd97a83715e60ae1139 48634 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170435/CIP007012.A0101.MT1.12.bam +CUC002 half ds n/a ERR4170441 PRJEB37518 SAMEA6850853 CUC002 ERS4578447 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CUC002.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/001/ERR4170441/ERR4170441.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/001/ERR4170441/ERR4170441.fastq.gz 455983 b89a1e48a4bf7e77e18dde80688103dc 32148 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170441/CUC002.A0101.MT1.1.bam +LAV001 half ds n/a ERR4170448 PRJEB37518 SAMEA6850860 LAV001 ERS4578454 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV001.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/008/ERR4170448/ERR4170448.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/008/ERR4170448/ERR4170448.fastq.gz 669780 622ee23336e9b3295f17555aa2fbc25a 49247 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170448/LAV001.A0101.MT1.1.bam +LAV006 half ds n/a ERR4170453 PRJEB37518 SAMEA6850865 LAV006 ERS4578459 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV006.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170453/ERR4170453.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170453/ERR4170453.fastq.gz 759194 229d289d778904311715472209a792ac 57636 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170453/LAV006.A0101.MT1.1.bam +LAV007 half ds n/a ERR4170454 PRJEB37518 SAMEA6850866 LAV007 ERS4578460 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV007.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170454/ERR4170454.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170454/ERR4170454.fastq.gz 967611 a97190384a04f191e05911e9933d7b18 71588 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170454/LAV007.A0101.MT1.1.bam +LAV008 half ds n/a ERR4170455 PRJEB37518 SAMEA6850867 LAV008 ERS4578461 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV008.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170455/ERR4170455.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170455/ERR4170455.fastq.gz 773093 d39466ad1db0ce43c06dd53984ecfc92 62495 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170455/LAV008.A0101.MT1.1.bam +LAV010 half ds n/a ERR4170457 PRJEB37518 SAMEA6850869 LAV010 ERS4578463 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV010.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/007/ERR4170457/ERR4170457.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/007/ERR4170457/ERR4170457.fastq.gz 227820 2fdd9b1bc3dcb7adc08a0a3df9b4f45d 14613 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170457/LAV010.A0101.MT1.1.bam +LAV011 half ds n/a ERR4170458 PRJEB37518 SAMEA6850870 LAV011 ERS4578464 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV011.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/008/ERR4170458/ERR4170458.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/008/ERR4170458/ERR4170458.fastq.gz 357938 1d8dc6fa474f9d7dfc9b5d6ff6561559 27778 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170458/LAV011.A0101.MT1.1.bam +LOI001 half ds n/a ERR4170460 PRJEB37518 SAMEA6850872 LOI001 ERS4578466 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LOI001.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/000/ERR4170460/ERR4170460.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/000/ERR4170460/ERR4170460.fastq.gz 128037 dcfa7dee2a9393daa94af92626f442a3 7606 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170460/LOI001.A0101.MT1.1.bam +PCA001 half ds n/a ERR4170462 PRJEB37518 SAMEA6850874 PCA001 ERS4578468 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PCA001.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170462/ERR4170462.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170462/ERR4170462.fastq.gz 78305 0c954c369bbae8b68a92043b6e3fd997 4409 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170462/PCA001.A0101.MT1.1.bam +PCA002 half ds n/a ERR4170463 PRJEB37518 SAMEA6850875 PCA002 ERS4578469 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PCA002.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170463/ERR4170463.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170463/ERR4170463.fastq.gz 286137 323ae59494eb8152d23394e92d4490c2 18415 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170463/PCA002.A0101.MT1.1.bam +PCV003 half ds n/a ERR4170469 PRJEB37518 SAMEA6850881 PCV003 ERS4578475 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PCV003.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/009/ERR4170469/ERR4170469.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/009/ERR4170469/ERR4170469.fastq.gz 707981 b08cc17a57d82893e1a894692056bb0b 47856 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170469/PCV003.A0101.MT1.1.bam +PCV004 half ds n/a ERR4170470 PRJEB37518 SAMEA6850882 PCV004 ERS4578476 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PCV004.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/000/ERR4170470/ERR4170470.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/000/ERR4170470/ERR4170470.fastq.gz 454992 13d606b931c2461bc8a87578844c992f 36771 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170470/PCV004.A0101.MT1.1.bam +PDI003 half ds n/a ERR4170471 PRJEB37518 SAMEA6850883 PDI003 ERS4578477 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDI003.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/001/ERR4170471/ERR4170471.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/001/ERR4170471/ERR4170471.fastq.gz 37792 426d7b475ca915bdfd123c81effa9e7a 1919 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170471/PDI003.A0101.MT1.1.bam +PDI008 half ds n/a ERR4170473 PRJEB37518 SAMEA6850885 PDI008 ERS4578479 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDI008.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170473/ERR4170473.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170473/ERR4170473.fastq.gz 421439 fa30d69dfa233be2b5115f20876bb4f8 29190 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170473/PDI008.A0101.MT1.1.bam +PDM001 half ds n/a ERR4170478 PRJEB37518 SAMEA6850890 PDM001 ERS4578484 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDM001.A0101.MT1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/008/ERR4170478/ERR4170478.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/008/ERR4170478/ERR4170478.fastq.gz 291970 a198757f5c6c385da6fbead66704391b 21443 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170478/PDM001.A0101.MT1.12.bam +PDM003 half ds n/a ERR4170480 PRJEB37518 SAMEA6850892 PDM003 ERS4578486 2020-06-03 2021-10-22 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDM003.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/000/ERR4170480/ERR4170480.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/000/ERR4170480/ERR4170480.fastq.gz 40680 1a73df21331efd1b597b4f3f695ec418 2093 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170480/PDM003.A0101.MT1.1.bam +PDM004 half ds n/a ERR4170481 PRJEB37518 SAMEA6850893 PDM004 ERS4578487 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDM004.B0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/001/ERR4170481/ERR4170481.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/001/ERR4170481/ERR4170481.fastq.gz 1072081 8ac749b5e5ddfc9872bdc537dc9e49db 86747 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170481/PDM004.B0101.MT1.1.bam +PDM006 half ds n/a ERR4170482 PRJEB37518 SAMEA6850894 PDM006 ERS4578488 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDM006.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170482/ERR4170482.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170482/ERR4170482.fastq.gz 86465 4afc3a80f2005507c29c2b29d314a477 5326 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170482/PDM006.A0101.MT1.1.bam +TIB002 half ds n/a ERR4170487 PRJEB37518 SAMEA6850899 TIB002 ERS4578493 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA TIB002.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/007/ERR4170487/ERR4170487.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/007/ERR4170487/ERR4170487.fastq.gz 244978 3d73739138bddcd246f948e749ac57de 16875 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170487/TIB002.A0101.MT1.1.bam +ALG001 minus ds n/a ERR4170302 PRJEB37518 SAMEA6850807 ALG001 ERS4578401 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA ALG001.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170302/ERR4170302.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170302/ERR4170302.fastq.gz 69836674 f9b0994296710cb51872cadff102e06e 1918610 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170302/ALG001.A0101.TF1.12.bam +CAA001003 half ds n/a ERR4170306 PRJEB37518 SAMEA6850811 CAA001003 ERS4578405 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAA001003.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170306/ERR4170306.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170306/ERR4170306.fastq.gz 336417609 d47ce87b6e072d1ebbc73827016c0630 9660049 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170306/CAA001003.TF1.1.bam +CAO017 half ds n/a ERR4170320 PRJEB37518 SAMEA6850825 CAO017 ERS4578419 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO017.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/000/ERR4170320/ERR4170320.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/000/ERR4170320/ERR4170320.fastq.gz 172411937 84d339404138c502c0735d3918910126 5316226 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170320/CAO017.A0101.TF1.1.bam +CAO019 half ds n/a ERR4170322 PRJEB37518 SAMEA6850827 CAO019 ERS4578421 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO019.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170322/ERR4170322.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170322/ERR4170322.fastq.gz 38535381 6739598a2c7d2ff93724dada3cba9c78 1189706 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170322/CAO019.A0101.TF1.1.bam +CAO020 half ds n/a ERR4170323 PRJEB37518 SAMEA6850828 CAO020 ERS4578422 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO020.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170323/ERR4170323.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170323/ERR4170323.fastq.gz 331805405 7205c54b0293f799345fc68bff460afb 10554376 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170323/CAO020.A0101.TF1.1.bam +CAO024 half ds n/a ERR4170327 PRJEB37518 SAMEA6850832 CAO024 ERS4578426 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO024.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/007/ERR4170327/ERR4170327.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/007/ERR4170327/ERR4170327.fastq.gz 331259122 c19005e8af4474ce840a4cf249dc0cbf 9822184 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170327/CAO024.A0101.TF1.1.bam +CAO028 half ds n/a ERR4170329 PRJEB37518 SAMEA6850834 CAO028 ERS4578428 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO028.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/009/ERR4170329/ERR4170329.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/009/ERR4170329/ERR4170329.fastq.gz 348766008 584733227e97ac60831cec2d95fd0bbb 9941855 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170329/CAO028.A0101.TF1.1.bam +CAO029 half ds n/a ERR4170330 PRJEB37518 SAMEA6850835 CAO029 ERS4578429 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO029.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/000/ERR4170330/ERR4170330.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/000/ERR4170330/ERR4170330.fastq.gz 365406842 a45726a4a87154165b135ec0a9a62a76 10256336 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170330/CAO029.A0101.TF1.1.bam +CDE002 half ds n/a ERR4170335 PRJEB37518 SAMEA6850840 CDE002 ERS4578434 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CDE002.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170335/ERR4170335.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170335/ERR4170335.fastq.gz 339284695 ecca5ec8972df273b010b16bea878cb8 9734510 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170335/CDE002.A0101.TF1.1.bam +CDE004 half ds n/a ERR4170337 PRJEB37518 SAMEA6850842 CDE004 ERS4578436 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CDE004.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/007/ERR4170337/ERR4170337.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/007/ERR4170337/ERR4170337.fastq.gz 224885546 82201552b0015ee1b6746c6e459ab210 6564052 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170337/CDE004.A0101.TF1.1.bam +CIP010 half ds n/a ERR4170345 PRJEB37518 SAMEA6850850 CIP010 ERS4578444 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CIP010.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170345/ERR4170345.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170345/ERR4170345.fastq.gz 16194987 af23e0dd96fdc7e40e8ed8cd9e0c2ff2 454423 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170345/CIP010.A0101.TF1.12.bam +CUC002 half ds n/a ERR4170348 PRJEB37518 SAMEA6850853 CUC002 ERS4578447 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CUC002.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/008/ERR4170348/ERR4170348.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/008/ERR4170348/ERR4170348.fastq.gz 305119476 f771c5d0062cbc36f20d4878c2da070a 8818770 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170348/CUC002.A0101.TF1.1.bam +CUC003 half ds n/a ERR4170349 PRJEB37518 SAMEA6850854 CUC003 ERS4578448 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CUC003.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/009/ERR4170349/ERR4170349.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/009/ERR4170349/ERR4170349.fastq.gz 359705340 2725195364cbd8ef8e77d800ae9d15bb 10197384 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170349/CUC003.A0101.TF1.1.bam +CUC004 half ds n/a ERR4170350 PRJEB37518 SAMEA6850855 CUC004 ERS4578449 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CUC004.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/000/ERR4170350/ERR4170350.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/000/ERR4170350/ERR4170350.fastq.gz 7572749 ed25847e7dc629fe6f949a4b2a563643 234771 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170350/CUC004.A0101.TF1.1.bam +GUY001 half ds n/a ERR4170352 PRJEB37518 SAMEA6850857 GUY001 ERS4578451 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUY001.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170352/ERR4170352.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170352/ERR4170352.fastq.gz 245435639 7ca3056d7ac29436fb58a21dbaa489b9 7440439 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170352/GUY001.A0101.TF1.1.bam +LAV005 half ds n/a ERR4170359 PRJEB37518 SAMEA6850864 LAV005 ERS4578458 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV005.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/009/ERR4170359/ERR4170359.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/009/ERR4170359/ERR4170359.fastq.gz 118961925 46f4c3386dd9fd4d17d4ac216ac910b7 3529476 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170359/LAV005.A0101.TF1.12.bam +LAV012 half ds n/a ERR4170366 PRJEB37518 SAMEA6850871 LAV012 ERS4578465 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV012.A0101.TF1.1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170366/ERR4170366.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170366/ERR4170366.fastq.gz 7848041 f7b51f189a7a9d1d75e08e8b35f52854 236322 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170366/LAV012.A0101.TF1.12.bam +MTO001 half ds n/a ERR4170368 PRJEB37518 SAMEA6850873 MTO001 ERS4578467 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA MTO001.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/008/ERR4170368/ERR4170368.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/008/ERR4170368/ERR4170368.fastq.gz 94895096 b57e772ee4b381888744d60b4811c6b4 2602210 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170368/MTO001.A0101.TF1.1.bam +PCA006 half ds n/a ERR4170371 PRJEB37518 SAMEA6850876 PCA006 ERS4578470 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PCA006.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/001/ERR4170371/ERR4170371.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/001/ERR4170371/ERR4170371.fastq.gz 19191651 88576b7d0711363b6525df325e5e611a 540685 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170371/PCA006.A0101.TF1.1.bam +PCA010 half ds n/a ERR4170373 PRJEB37518 SAMEA6850878 PCA010 ERS4578472 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PCA010.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170373/ERR4170373.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170373/ERR4170373.fastq.gz 3294912 62fc58c6941a15cf68cfa29f68e4e1d9 90485 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170373/PCA010.A0101.TF1.1.bam +PDI006 half ds n/a ERR4170379 PRJEB37518 SAMEA6850884 PDI006 ERS4578478 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDI006.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/009/ERR4170379/ERR4170379.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/009/ERR4170379/ERR4170379.fastq.gz 17627927 a266069df67c0e496a62c5c0b5b7f98e 531613 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170379/PDI006.A0101.TF1.1.bam +PDI008 half ds n/a ERR4170380 PRJEB37518 SAMEA6850885 PDI008 ERS4578479 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDI008.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/000/ERR4170380/ERR4170380.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/000/ERR4170380/ERR4170380.fastq.gz 141860837 b43bd1b10ccfe79d98b1f72e1ca6de36 4036953 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170380/PDI008.A0101.TF1.1.bam +PDI012013 half ds n/a ERR4170384 PRJEB37518 SAMEA6850889 PDI012013 ERS4578483 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDI012013.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170384/ERR4170384.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170384/ERR4170384.fastq.gz 206220600 644b63822f1b91412d857e366049d9b3 6175970 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170384/PDI012013.A0101.TF1.1.bam +PDM006 half ds n/a ERR4170389 PRJEB37518 SAMEA6850894 PDM006 ERS4578488 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDM006.A0101.TF2.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/009/ERR4170389/ERR4170389.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/009/ERR4170389/ERR4170389.fastq.gz 79292438 9f788e6cc3a9b4a6150bf8f59f760daf 2338091 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170389/PDM006.A0101.TF2..bam +PDM010 half ds n/a ERR4170392 PRJEB37518 SAMEA6850897 PDM010 ERS4578491 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDM010.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170392/ERR4170392.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170392/ERR4170392.fastq.gz 84833285 3851c3ced51308d4f3b5ba48d54c69d6 2518706 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170392/PDM010.A0101.TF1.1.bam +ALG003 minus ds n/a ERR4170397 PRJEB37518 SAMEA6850809 ALG003 ERS4578403 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA ALG003.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/007/ERR4170397/ERR4170397.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/007/ERR4170397/ERR4170397.fastq.gz 725032 23d5d1231df4724ad114488ce1a34942 48683 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170397/ALG003.A0101.MT1.1.bam +ALG004 minus ds n/a ERR4170398 PRJEB37518 SAMEA6850810 ALG004 ERS4578404 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA ALG004.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/008/ERR4170398/ERR4170398.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/008/ERR4170398/ERR4170398.fastq.gz 272678 65b161ff7ec06be1583f5114b1cf64da 16331 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170398/ALG004.A0101.MT1.1.bam +CAA001003 half ds n/a ERR4170399 PRJEB37518 SAMEA6850811 CAA001003 ERS4578405 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAA001003.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/009/ERR4170399/ERR4170399.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/009/ERR4170399/ERR4170399.fastq.gz 3099167 fa760cf14e10216aa1e4346a17acf2bd 231872 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170399/CAA001003.A0101.MT1.1.bam +CAO009013 half ds n/a ERR4170406 PRJEB37518 SAMEA6850818 CAO009013 ERS4578412 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO009013.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170406/ERR4170406.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170406/ERR4170406.fastq.gz 542412 bd6c4e1cfc2a73889d614e92daeb6583 38775 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170406/CAO009013.A0101.MT1.1.bam +CAO014 half ds n/a ERR4170410 PRJEB37518 SAMEA6850822 CAO014 ERS4578416 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO014.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/000/ERR4170410/ERR4170410.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/000/ERR4170410/ERR4170410.fastq.gz 194152 d5672bdea7a68d25db68a95a7496352b 12327 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170410/CAO014.A0101.MT1.1.bam +CAO016 half ds n/a ERR4170412 PRJEB37518 SAMEA6850824 CAO016 ERS4578418 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO016.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170412/ERR4170412.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170412/ERR4170412.fastq.gz 108750 183d62e2bfc7f71f137af4efd08f7417 7144 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170412/CAO016.A0101.MT1.1.bam +CAO018 half ds n/a ERR4170414 PRJEB37518 SAMEA6850826 CAO018 ERS4578420 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO018.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170414/ERR4170414.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170414/ERR4170414.fastq.gz 3209 b30bd1cb839f2a5f4d2c0c5bae887dbc 115 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170414/CAO018.A0101.MT1.1.bam +CAO022026 half ds n/a ERR4170418 PRJEB37518 SAMEA6850830 CAO022026 ERS4578424 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO022026.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/008/ERR4170418/ERR4170418.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/008/ERR4170418/ERR4170418.fastq.gz 349320 239e2c44ba7f612fb78475b76dbbee5c 28239 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170418/CAO022026.A0101.MT1.1.bam +CAO023025 half ds n/a ERR4170419 PRJEB37518 SAMEA6850831 CAO023025 ERS4578425 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO023025.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/009/ERR4170419/ERR4170419.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/009/ERR4170419/ERR4170419.fastq.gz 494960 1c89bad150331b75ae4ac607c8d44e6f 36954 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170419/CAO023025.A0101.MT1.1.bam +CAO030 half ds n/a ERR4170424 PRJEB37518 SAMEA6850836 CAO030 ERS4578430 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO030.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170424/ERR4170424.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170424/ERR4170424.fastq.gz 356227 7916840841c565e5a8ee7f2bfd460337 24190 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170424/CAO030.A0101.MT1.1.bam +CAO032 half ds n/a ERR4170426 PRJEB37518 SAMEA6850838 CAO032 ERS4578432 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO032.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170426/ERR4170426.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170426/ERR4170426.fastq.gz 393897 14c7aa15f3b2852cf9ba72059d58b627 25167 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170426/CAO032.A0101.MT1.1.bam +CDE001 half ds n/a ERR4170427 PRJEB37518 SAMEA6850839 CDE001 ERS4578433 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CDE001.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/007/ERR4170427/ERR4170427.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/007/ERR4170427/ERR4170427.fastq.gz 416960 9ef23b6569257ca8fd5b587476d51e02 32716 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170427/CDE001.A0101.MT1.1.bam +CDE002 half ds n/a ERR4170428 PRJEB37518 SAMEA6850840 CDE002 ERS4578434 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CDE002.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/008/ERR4170428/ERR4170428.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/008/ERR4170428/ERR4170428.fastq.gz 433197 b4d120fea8efedfaa8ab0323ef236890 32703 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170428/CDE002.A0101.MT1.1.bam +CDE003 half ds n/a ERR4170429 PRJEB37518 SAMEA6850841 CDE003 ERS4578435 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CDE003.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/009/ERR4170429/ERR4170429.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/009/ERR4170429/ERR4170429.fastq.gz 437870 d22e8f7efabd11eb4e0d6bc94585e5b6 32831 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170429/CDE003.A0101.MT1.1.bam +CDE005 half ds n/a ERR4170431 PRJEB37518 SAMEA6850843 CDE005 ERS4578437 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CDE005.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/001/ERR4170431/ERR4170431.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/001/ERR4170431/ERR4170431.fastq.gz 463162 bb4070270c762df72f913c466a5a895e 30646 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170431/CDE005.A0101.MT1.1.bam +CIP001 half ds n/a ERR4170432 PRJEB37518 SAMEA6850844 CIP001 ERS4578438 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CIP001.A0101.TF1.1mt Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170432/ERR4170432.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170432/ERR4170432.fastq.gz 46839 ea058e711b5d4d8a04853f42c0a3183b 2426 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170432/CIP001.A0101.TF1.1mt.bam +CIP009 half ds n/a ERR4170437 PRJEB37518 SAMEA6850849 CIP009 ERS4578443 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CIP009.A0101.MT1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/007/ERR4170437/ERR4170437.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/007/ERR4170437/ERR4170437.fastq.gz 481055 8f454c8100d2f4955c90486f591d421d 29945 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170437/CIP009.A0101.MT1.12.bam +CUC001 half ds n/a ERR4170440 PRJEB37518 SAMEA6850852 CUC001 ERS4578446 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CUC001.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/000/ERR4170440/ERR4170440.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/000/ERR4170440/ERR4170440.fastq.gz 10227 95699e77a97c4ce454c813ee639d296c 508 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170440/CUC001.A0101.MT1.1.bam +CUC003 half ds n/a ERR4170442 PRJEB37518 SAMEA6850854 CUC003 ERS4578448 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CUC003.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170442/ERR4170442.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170442/ERR4170442.fastq.gz 425977 46f63ddb58a3127dc680ef2a71b26454 32515 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170442/CUC003.A0101.MT1.1.bam +GUY002 half ds n/a ERR4170446 PRJEB37518 SAMEA6850858 GUY002 ERS4578452 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUY002.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170446/ERR4170446.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170446/ERR4170446.fastq.gz 255045 469f32f501c1bb99457ae464fdcebd19 17031 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170446/GUY002.A0101.MT1.1.bam +LAV002 half ds n/a ERR4170449 PRJEB37518 SAMEA6850861 LAV002 ERS4578455 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV002.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/009/ERR4170449/ERR4170449.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/009/ERR4170449/ERR4170449.fastq.gz 1528261 cdca7efe90a24c3400a97ea53128b096 111461 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170449/LAV002.A0101.MT1.1.bam +LAV003 half ds n/a ERR4170450 PRJEB37518 SAMEA6850862 LAV003 ERS4578456 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV003.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/000/ERR4170450/ERR4170450.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/000/ERR4170450/ERR4170450.fastq.gz 482689 b2f56cf9b9d916e177a0b1244649efb9 32779 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170450/LAV003.A0101.MT1.1.bam +LAV005 half ds n/a ERR4170452 PRJEB37518 SAMEA6850864 LAV005 ERS4578458 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV005.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170452/ERR4170452.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170452/ERR4170452.fastq.gz 826278 3a98f4120a0cfb4331d816a16d77aa1b 65693 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170452/LAV005.A0101.MT1.1.bam +LAV009 half ds n/a ERR4170456 PRJEB37518 SAMEA6850868 LAV009 ERS4578462 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV009.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170456/ERR4170456.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170456/ERR4170456.fastq.gz 1493937 b34fe429cb463c89d88eadfbc44ea802 120257 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170456/LAV009.A0101.MT1.1.bam +LAV012 half ds n/a ERR4170459 PRJEB37518 SAMEA6850871 LAV012 ERS4578465 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV012.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/009/ERR4170459/ERR4170459.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/009/ERR4170459/ERR4170459.fastq.gz 748337 c4f6fa8aaf743f52ebc13d74bb239fda 52811 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170459/LAV012.A0101.MT1.1.bam +MTO001 half ds n/a ERR4170461 PRJEB37518 SAMEA6850873 MTO001 ERS4578467 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA MTO001.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/001/ERR4170461/ERR4170461.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/001/ERR4170461/ERR4170461.fastq.gz 469447 d5ff1d541d31bd77499f5464359e6404 30974 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170461/MTO001.A0101.MT1.1.bam +PCA006 half ds n/a ERR4170464 PRJEB37518 SAMEA6850876 PCA006 ERS4578470 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PCA006.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170464/ERR4170464.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170464/ERR4170464.fastq.gz 369420 658533b007f83d07c84e642e8a958595 26078 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170464/PCA006.A0101.MT1.1.bam +PCA010 half ds n/a ERR4170466 PRJEB37518 SAMEA6850878 PCA010 ERS4578472 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PCA010.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170466/ERR4170466.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170466/ERR4170466.fastq.gz 53292 44b3da13b8b195f52a807c815c868214 3090 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170466/PCA010.A0101.MT1.1.bam +PDI006 half ds n/a ERR4170472 PRJEB37518 SAMEA6850884 PDI006 ERS4578478 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDI006.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170472/ERR4170472.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170472/ERR4170472.fastq.gz 51549 6e1d6606cbd8fefe5f0158413d923dba 2921 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170472/PDI006.A0101.MT1.1.bam +PDI010 half ds n/a ERR4170475 PRJEB37518 SAMEA6850887 PDI010 ERS4578481 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDI010.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170475/ERR4170475.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170475/ERR4170475.fastq.gz 626144 cb7097ec4fae73e999dd7388a4e05d39 47757 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170475/PDI010.A0101.MT1.1.bam +PDI011 half ds n/a ERR4170476 PRJEB37518 SAMEA6850888 PDI011 ERS4578482 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDI011.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170476/ERR4170476.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170476/ERR4170476.fastq.gz 283223 96be4960ea9e7f364b0fe60fd832a194 19610 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170476/PDI011.A0101.MT1.1.bam +PDM002 half ds n/a ERR4170479 PRJEB37518 SAMEA6850891 PDM002 ERS4578485 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDM002.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/009/ERR4170479/ERR4170479.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/009/ERR4170479/ERR4170479.fastq.gz 250377 0ef70812ccc9c6132931036bf94f29f1 21346 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170479/PDM002.A0101.MT1.1.bam +TIB001 half ds n/a ERR4170486 PRJEB37518 SAMEA6850898 TIB001 ERS4578492 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA TIB001.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170486/ERR4170486.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170486/ERR4170486.fastq.gz 131974 29b7b8af256b491610c06ec60f69cb52 8046 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170486/TIB001.A0101.MT1.1.bam +ALG004 minus ds n/a ERR4170305 PRJEB37518 SAMEA6850810 ALG004 ERS4578404 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA ALG004.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170305/ERR4170305.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170305/ERR4170305.fastq.gz 67599236 f5166e22ffc578f8380c3ac723a39b29 1860300 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170305/ALG004.A0101.TF1.12.bam +CAO001 half ds n/a ERR4170308 PRJEB37518 SAMEA6850813 CAO001 ERS4578407 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO001.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/008/ERR4170308/ERR4170308.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/008/ERR4170308/ERR4170308.fastq.gz 106301181 c403f8e9d278fc18cb65c69c0291b9f9 2935895 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170308/CAO001.A0101.TF1.1.bam +CAO004 half ds n/a ERR4170310 PRJEB37518 SAMEA6850815 CAO004 ERS4578409 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO004.B0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/000/ERR4170310/ERR4170310.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/000/ERR4170310/ERR4170310.fastq.gz 7743977 e51f1d6cb56c2336e487fcc214c7ebc1 206984 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170310/CAO004.B0101.TF1.1.bam +CAO009013 half ds n/a ERR4170313 PRJEB37518 SAMEA6850818 CAO009013 ERS4578412 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO009013.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170313/ERR4170313.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170313/ERR4170313.fastq.gz 467885649 973986ee942f6f69899816bbd7934a37 13835333 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170313/CAO009013.TF1.1.bam +CAO010 half ds n/a ERR4170314 PRJEB37518 SAMEA6850819 CAO010 ERS4578413 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO010.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170314/ERR4170314.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170314/ERR4170314.fastq.gz 66437741 61ba736e5546e36e435c87e662f5ac2f 1738105 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170314/CAO010.A0101.TF1.1.bam +CAO011 half ds n/a ERR4170315 PRJEB37518 SAMEA6850820 CAO011 ERS4578414 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO011.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170315/ERR4170315.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170315/ERR4170315.fastq.gz 342440375 139c4b05b6edd8cc3aba85a4176d3a90 10398612 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170315/CAO011.A0101.TF1.1.bam +CAO014 half ds n/a ERR4170317 PRJEB37518 SAMEA6850822 CAO014 ERS4578416 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO014.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/007/ERR4170317/ERR4170317.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/007/ERR4170317/ERR4170317.fastq.gz 145575670 8a6717cd11f4272980caf1b651058dba 4251650 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170317/CAO014.A0101.TF1.1.bam +CAO016 half ds n/a ERR4170319 PRJEB37518 SAMEA6850824 CAO016 ERS4578418 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO016.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/009/ERR4170319/ERR4170319.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/009/ERR4170319/ERR4170319.fastq.gz 97318787 6d4443496e94b4e57383e1fd6856c5ce 3090605 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170319/CAO016.A0101.TF1.1.bam +CAO018 half ds n/a ERR4170321 PRJEB37518 SAMEA6850826 CAO018 ERS4578420 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO018.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/001/ERR4170321/ERR4170321.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/001/ERR4170321/ERR4170321.fastq.gz 3608837 935fcb5760e7aaa32acf590dccd47344 98999 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170321/CAO018.A0101.TF1.1.bam +CAO021 half ds n/a ERR4170324 PRJEB37518 SAMEA6850829 CAO021 ERS4578423 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO021.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170324/ERR4170324.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170324/ERR4170324.fastq.gz 364456340 7b17023b4f07ca83fd8c041b023c2766 10586173 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170324/CAO021.A0101.TF1.1.bam +CAO023025 half ds n/a ERR4170326 PRJEB37518 SAMEA6850831 CAO023025 ERS4578425 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO023025.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170326/ERR4170326.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170326/ERR4170326.fastq.gz 591960917 2f04112759bf7b6532b292ae03378de1 18177909 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170326/CAO023025.TF1.1.bam +CAO032 half ds n/a ERR4170333 PRJEB37518 SAMEA6850838 CAO032 ERS4578432 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO032.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170333/ERR4170333.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170333/ERR4170333.fastq.gz 180583606 fffb13468e6ba3149208b1c5759fa64d 4991613 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170333/CAO032.A0101.TF1.1.bam +CDE003 half ds n/a ERR4170336 PRJEB37518 SAMEA6850841 CDE003 ERS4578435 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CDE003.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170336/ERR4170336.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170336/ERR4170336.fastq.gz 276513398 9665bc985e05ae5eb6e80efc390f91f3 7797854 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170336/CDE003.A0101.TF1.1.bam +CIP002 half ds n/a ERR4170340 PRJEB37518 SAMEA6850845 CIP002 ERS4578439 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CIP002.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/000/ERR4170340/ERR4170340.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/000/ERR4170340/ERR4170340.fastq.gz 27834792 cc9ae9af8f6591856d69046f2f52cd97 770863 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170340/CIP002.A0101.TF1.12.bam +CIP007012 half ds n/a ERR4170342 PRJEB37518 SAMEA6850847 CIP007012 ERS4578441 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CIP007012.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170342/ERR4170342.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170342/ERR4170342.fastq.gz 17839973 f35fefc6bedb14ddc97746de1973454d 515893 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170342/CIP007012.TF1.12.bam +CUC001 half ds n/a ERR4170347 PRJEB37518 SAMEA6850852 CUC001 ERS4578446 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CUC001.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/007/ERR4170347/ERR4170347.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/007/ERR4170347/ERR4170347.fastq.gz 2924703 fdeb09abd33679c79db4392e6edf260b 95835 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170347/CUC001.A0101.TF1.1.bam +GUY003 half ds n/a ERR4170354 PRJEB37518 SAMEA6850859 GUY003 ERS4578453 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUY003.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170354/ERR4170354.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170354/ERR4170354.fastq.gz 11620195 11c84a6a57f01a4a3ce8d6a8b9af02c7 372871 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170354/GUY003.A0101.TF1.1.bam +LAV001 half ds n/a ERR4170355 PRJEB37518 SAMEA6850860 LAV001 ERS4578454 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV001.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170355/ERR4170355.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170355/ERR4170355.fastq.gz 148436272 9196d071a7a225e69df914ecfebf3bdc 4247340 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170355/LAV001.A0101.TF1.12.bam +LAV002 half ds n/a ERR4170356 PRJEB37518 SAMEA6850861 LAV002 ERS4578455 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV002.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170356/ERR4170356.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170356/ERR4170356.fastq.gz 309634610 7f5b143c839b543a1a0d352f4dd08f6b 9653356 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170356/LAV002.A0101.TF1.12.bam +LAV003 half ds n/a ERR4170357 PRJEB37518 SAMEA6850862 LAV003 ERS4578456 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV003.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/007/ERR4170357/ERR4170357.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/007/ERR4170357/ERR4170357.fastq.gz 177548710 18177da57344c5bd0becc3d57a7c07a2 5307686 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170357/LAV003.A0101.TF1.12.bam +LAV004 half ds n/a ERR4170358 PRJEB37518 SAMEA6850863 LAV004 ERS4578457 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV004.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/008/ERR4170358/ERR4170358.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/008/ERR4170358/ERR4170358.fastq.gz 108436700 c4b8b66813507b1ffe8ca8fb44f3aba0 3209676 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170358/LAV004.A0101.TF1.12.bam +LAV007 half ds n/a ERR4170361 PRJEB37518 SAMEA6850866 LAV007 ERS4578460 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV007.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/001/ERR4170361/ERR4170361.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/001/ERR4170361/ERR4170361.fastq.gz 80940650 347205a695e077ce3f29e9b381d9c742 2270546 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170361/LAV007.A0101.TF1.12.bam +LAV008 half ds n/a ERR4170362 PRJEB37518 SAMEA6850867 LAV008 ERS4578461 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV008.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170362/ERR4170362.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170362/ERR4170362.fastq.gz 32295795 903e7ff1817bce1c6882036aa37f5b94 902612 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170362/LAV008.A0101.TF1.12.bam +LAV009 half ds n/a ERR4170363 PRJEB37518 SAMEA6850868 LAV009 ERS4578462 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV009.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170363/ERR4170363.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170363/ERR4170363.fastq.gz 10356554 b94b1fa0ef21af16542ecd888c07d228 321433 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170363/LAV009.A0101.TF1.12.bam +LAV010 half ds n/a ERR4170364 PRJEB37518 SAMEA6850869 LAV010 ERS4578463 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV010.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170364/ERR4170364.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170364/ERR4170364.fastq.gz 80626022 3c87eb2e508b3cf6e77f097f81f2b76f 2271056 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170364/LAV010.A0101.TF1.12.bam +LAV011 half ds n/a ERR4170365 PRJEB37518 SAMEA6850870 LAV011 ERS4578464 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV011.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170365/ERR4170365.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170365/ERR4170365.fastq.gz 16279581 f85e0063753ff25b538db4b6b2322341 468086 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170365/LAV011.A0101.TF1.12.bam +LOI001 half ds n/a ERR4170367 PRJEB37518 SAMEA6850872 LOI001 ERS4578466 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LOI001.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/007/ERR4170367/ERR4170367.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/007/ERR4170367/ERR4170367.fastq.gz 12718338 5677185ab8f01f2d34f168646e41113f 351552 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170367/LOI001.A0101.TF1.12.bam +PCA001 half ds n/a ERR4170369 PRJEB37518 SAMEA6850874 PCA001 ERS4578468 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PCA001.A0101.TF1.1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/009/ERR4170369/ERR4170369.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/009/ERR4170369/ERR4170369.fastq.gz 12788904 3df65822481085c5683c59cc324fe8fe 371917 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170369/PCA001.A0101.TF1.12.bam +PCV001 half ds n/a ERR4170374 PRJEB37518 SAMEA6850879 PCV001 ERS4578473 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PCV001.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170374/ERR4170374.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170374/ERR4170374.fastq.gz 61319696 e07b31b990bb2df78898b00f74b3b7f4 1684492 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170374/PCV001.A0101.TF1.12.bam +PCV002 half ds n/a ERR4170375 PRJEB37518 SAMEA6850880 PCV002 ERS4578474 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PCV002.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170375/ERR4170375.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170375/ERR4170375.fastq.gz 95211759 d348c51464a4f23fb5e41ac1017f69a0 2694546 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170375/PCV002.A0101.TF1.12.bam +PCV003 half ds n/a ERR4170376 PRJEB37518 SAMEA6850881 PCV003 ERS4578475 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PCV003.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170376/ERR4170376.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170376/ERR4170376.fastq.gz 63623998 5691232e01ee9c01b413bd26d01c9124 1785447 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170376/PCV003.A0101.TF1.12.bam +PCV004 half ds n/a ERR4170377 PRJEB37518 SAMEA6850882 PCV004 ERS4578476 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PCV004.A0101.TF1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/007/ERR4170377/ERR4170377.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/007/ERR4170377/ERR4170377.fastq.gz 18267759 0641e6de6860a88d24000332dfbd7da7 511416 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170377/PCV004.A0101.TF1.12.bam +PDI009 half ds n/a ERR4170381 PRJEB37518 SAMEA6850886 PDI009 ERS4578480 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDI009.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/001/ERR4170381/ERR4170381.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/001/ERR4170381/ERR4170381.fastq.gz 8618648 c1bc2ccfe78ce91559744a3a7912b8a0 235931 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170381/PDI009.A0101.TF1.1.bam +PDM003 half ds n/a ERR4170387 PRJEB37518 SAMEA6850892 PDM003 ERS4578486 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDM003.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/007/ERR4170387/ERR4170387.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/007/ERR4170387/ERR4170387.fastq.gz 11426471 a25fc839b7ac9e105fb23ccce64559fd 339980 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170387/PDM003.A0101.TF1.1.bam +PDM004 half ds n/a ERR4170388 PRJEB37518 SAMEA6850893 PDM004 ERS4578487 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDM004.B0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/008/ERR4170388/ERR4170388.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/008/ERR4170388/ERR4170388.fastq.gz 171124761 9fb1a2c69d410114495ead565985ee73 5195873 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170388/PDM004.B0101.TF1.1.bam +PDM009 half ds n/a ERR4170391 PRJEB37518 SAMEA6850896 PDM009 ERS4578490 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDM009.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/001/ERR4170391/ERR4170391.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/001/ERR4170391/ERR4170391.fastq.gz 49477414 772319aaeae14444af3a4c0fd90cbd76 1525063 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170391/PDM009.A0101.TF1.1.bam +TIB001 half ds n/a ERR4170393 PRJEB37518 SAMEA6850898 TIB001 ERS4578492 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA TIB001.A0101.TF1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170393/ERR4170393.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170393/ERR4170393.fastq.gz 13203219 4777f67367292f783f2b78ce372a454d 349889 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170393/TIB001.A0101.TF1.1.bam +ALG001 minus ds n/a ERR4170395 PRJEB37518 SAMEA6850807 ALG001 ERS4578401 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA ALG001.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170395/ERR4170395.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170395/ERR4170395.fastq.gz 749280 de51f9def144a42ec9544d2270e40bee 47005 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170395/ALG001.A0101.MT1.1.bam +CAO004 half ds n/a ERR4170403 PRJEB37518 SAMEA6850815 CAO004 ERS4578409 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO004.B0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170403/ERR4170403.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170403/ERR4170403.fastq.gz 220340 218b63fd93e623dc6b359feb1f73f12b 15596 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170403/CAO004.B0101.MT1.1.bam +CAO006 half ds n/a ERR4170404 PRJEB37518 SAMEA6850816 CAO006 ERS4578410 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO006.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170404/ERR4170404.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170404/ERR4170404.fastq.gz 347880 b22d642add296999cc2f63dba4d06c62 23291 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170404/CAO006.A0101.MT1.1.bam +CAO011 half ds n/a ERR4170408 PRJEB37518 SAMEA6850820 CAO011 ERS4578414 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO011.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/008/ERR4170408/ERR4170408.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/008/ERR4170408/ERR4170408.fastq.gz 471276 12117ea445e21a60cf26187aaba4f06b 31066 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170408/CAO011.A0101.MT1.1.bam +CAO012 half ds n/a ERR4170409 PRJEB37518 SAMEA6850821 CAO012 ERS4578415 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO012.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/009/ERR4170409/ERR4170409.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/009/ERR4170409/ERR4170409.fastq.gz 453725 9cbe9d65c375a5ae71d3473036861b35 31759 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170409/CAO012.A0101.MT1.1.bam +CAO017 half ds n/a ERR4170413 PRJEB37518 SAMEA6850825 CAO017 ERS4578419 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO017.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170413/ERR4170413.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170413/ERR4170413.fastq.gz 363540 20daf35e601e417c2df7aaad89caeb50 24482 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170413/CAO017.A0101.MT1.1.bam +CAO020 half ds n/a ERR4170416 PRJEB37518 SAMEA6850828 CAO020 ERS4578422 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO020.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170416/ERR4170416.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170416/ERR4170416.fastq.gz 459894 280617520cee63e52b0393057756e79f 30539 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170416/CAO020.A0101.MT1.1.bam +CAO027 half ds n/a ERR4170421 PRJEB37518 SAMEA6850833 CAO027 ERS4578427 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO027.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/001/ERR4170421/ERR4170421.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/001/ERR4170421/ERR4170421.fastq.gz 447410 106c76e34255ad29594ecc4c2abb7f4c 30522 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170421/CAO027.A0101.MT1.1.bam +CAO028 half ds n/a ERR4170422 PRJEB37518 SAMEA6850834 CAO028 ERS4578428 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CAO028.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/002/ERR4170422/ERR4170422.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/002/ERR4170422/ERR4170422.fastq.gz 464717 ed319e3afa1baf1c82983f4e5d57d282 32860 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170422/CAO028.A0101.MT1.1.bam +CDE004 half ds n/a ERR4170430 PRJEB37518 SAMEA6850842 CDE004 ERS4578436 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CDE004.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/000/ERR4170430/ERR4170430.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/000/ERR4170430/ERR4170430.fastq.gz 321623 74b4a2f9158bfe5f732450faf8fe7e69 20389 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170430/CDE004.A0101.MT1.1.bam +CIP008 half ds n/a ERR4170436 PRJEB37518 SAMEA6850848 CIP008 ERS4578442 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CIP008.A0101.MT1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/006/ERR4170436/ERR4170436.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/006/ERR4170436/ERR4170436.fastq.gz 817379 f031f3ac76f088ad0d44117ae461cf2b 46677 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170436/CIP008.A0101.MT1.12.bam +CIP010 half ds n/a ERR4170438 PRJEB37518 SAMEA6850850 CIP010 ERS4578444 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CIP010.A0101.MT1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/008/ERR4170438/ERR4170438.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/008/ERR4170438/ERR4170438.fastq.gz 395455 43e71bab77b53309c13125cd5e3fb491 24509 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170438/CIP010.A0101.MT1.12.bam +CIP011 half ds n/a ERR4170439 PRJEB37518 SAMEA6850851 CIP011 ERS4578445 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CIP011.A0101.MT1.12 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/009/ERR4170439/ERR4170439.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/009/ERR4170439/ERR4170439.fastq.gz 934199 233343b65c7e4a8322d96fc18f510f5d 54735 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170439/CIP011.A0101.MT1.12.bam +CUC004 half ds n/a ERR4170443 PRJEB37518 SAMEA6850855 CUC004 ERS4578449 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA CUC004.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170443/ERR4170443.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170443/ERR4170443.fastq.gz 31155 8652280f83dcabb6ebf9624246a79161 1691 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170443/CUC004.A0101.MT1.1.bam +ELM001 half ds n/a ERR4170444 PRJEB37518 SAMEA6850856 ELM001 ERS4578450 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA ELM001.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170444/ERR4170444.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170444/ERR4170444.fastq.gz 3758557 0e4745f88bb83f927550b2a71a7d3efa 276005 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170444/ELM001.A0101.MT1.1.bam +GUY001 half ds n/a ERR4170445 PRJEB37518 SAMEA6850857 GUY001 ERS4578451 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUY001.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170445/ERR4170445.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170445/ERR4170445.fastq.gz 408047 d9a5129fdbb069afb24e8ae3c3145e89 26514 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170445/GUY001.A0101.MT1.1.bam +GUY003 half ds n/a ERR4170447 PRJEB37518 SAMEA6850859 GUY003 ERS4578453 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUY003.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/007/ERR4170447/ERR4170447.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/007/ERR4170447/ERR4170447.fastq.gz 172241 666128d9d945452c865a8c376a737774 11543 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170447/GUY003.A0101.MT1.1.bam +LAV004 half ds n/a ERR4170451 PRJEB37518 SAMEA6850863 LAV004 ERS4578457 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA LAV004.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/001/ERR4170451/ERR4170451.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/001/ERR4170451/ERR4170451.fastq.gz 879226 10f634b4caf67b9de362e4a4bda2d172 72601 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170451/LAV004.A0101.MT1.1.bam +PCA009 half ds n/a ERR4170465 PRJEB37518 SAMEA6850877 PCA009 ERS4578471 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PCA009.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170465/ERR4170465.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170465/ERR4170465.fastq.gz 153528 7ced8555fe0c27562e657b85ce76c087 9742 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170465/PCA009.A0101.MT1.1.bam +PCV001 half ds n/a ERR4170467 PRJEB37518 SAMEA6850879 PCV001 ERS4578473 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PCV001.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/007/ERR4170467/ERR4170467.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/007/ERR4170467/ERR4170467.fastq.gz 1116580 2802bf9ba41136af6b2675f8db4aaf7f 83300 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170467/PCV001.A0101.MT1.1.bam +PCV002 half ds n/a ERR4170468 PRJEB37518 SAMEA6850880 PCV002 ERS4578474 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PCV002.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/008/ERR4170468/ERR4170468.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/008/ERR4170468/ERR4170468.fastq.gz 716508 799267cdf7b8358d8782047cd428df02 47788 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170468/PCV002.A0101.MT1.1.bam +PDI009 half ds n/a ERR4170474 PRJEB37518 SAMEA6850886 PDI009 ERS4578480 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDI009.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170474/ERR4170474.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170474/ERR4170474.fastq.gz 24253 de9e7cd30702f0d50606f109083bd353 1103 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170474/PDI009.A0101.MT1.1.bam +PDI012013 half ds n/a ERR4170477 PRJEB37518 SAMEA6850889 PDI012013 ERS4578483 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDI012013.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/007/ERR4170477/ERR4170477.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/007/ERR4170477/ERR4170477.fastq.gz 586828 905d4ed5fefeb8c3bb1b7f1016dfbf7c 43468 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170477/PDI012013.A0101.MT1.1.bam +PDM008 half ds n/a ERR4170483 PRJEB37518 SAMEA6850895 PDM008 ERS4578489 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDM008.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/003/ERR4170483/ERR4170483.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/003/ERR4170483/ERR4170483.fastq.gz 191460 26039a9d20639b903d6b33bd8997dcb2 14318 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170483/PDM008.A0101.MT1.1.bam +PDM009 half ds n/a ERR4170484 PRJEB37518 SAMEA6850896 PDM009 ERS4578490 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDM009.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/004/ERR4170484/ERR4170484.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/004/ERR4170484/ERR4170484.fastq.gz 208065 022440e3d6009443edf653ae93d01097 15377 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170484/PDM009.A0101.MT1.1.bam +PDM010 half ds n/a ERR4170485 PRJEB37518 SAMEA6850897 PDM010 ERS4578491 2020-06-03 2020-05-20 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA PDM010.A0101.MT1.1 Targeted-Capture ftp.sra.ebi.ac.uk/vol1/fastq/ERR417/005/ERR4170485/ERR4170485.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR417/005/ERR4170485/ERR4170485.fastq.gz 211367 c98019117d35ceeff5f4900168d081c2 14818 ftp.sra.ebi.ac.uk/vol1/run/ERR417/ERR4170485/PDM010.A0101.MT1.1.bam From fdc6c233a545916ca671bfe25da74dc4bf650be2 Mon Sep 17 00:00:00 2001 From: Thiseas Christos Lamnidis Date: Tue, 25 Jul 2023 15:50:51 +0200 Subject: [PATCH 4/6] Add 2021_Yaka_Anatolia ssf --- .../2021_Yaka_Anatolia/2021_Yaka_Anatolia.ssf | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 packages/2021_Yaka_Anatolia/2021_Yaka_Anatolia.ssf diff --git a/packages/2021_Yaka_Anatolia/2021_Yaka_Anatolia.ssf b/packages/2021_Yaka_Anatolia/2021_Yaka_Anatolia.ssf new file mode 100644 index 0000000..48c67f1 --- /dev/null +++ b/packages/2021_Yaka_Anatolia/2021_Yaka_Anatolia.ssf @@ -0,0 +1,23 @@ +poseidon_IDs udg library_built notes run_accession study_accession sample_accession sample_alias secondary_sample_accession first_public last_updated instrument_model library_layout library_source instrument_platform library_name library_strategy fastq_ftp fastq_aspera fastq_bytes fastq_md5 read_count submitted_ftp +Ash128 minus ds n/a ERR4332637 PRJEB39316 SAMEA7050456 4 ERS4811086 2021-04-11 2020-07-10 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA Ash128_all WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/007/ERR4332637/ERR4332637.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/007/ERR4332637/ERR4332637.fastq.gz 9236424742 0ab64459acd809b0ae82c20ea82dacca 302487376 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332637/Ash128_all.merged.hs37d5.fa.cons.90perc.bam +pch034 minus ds n/a ERR4332641 PRJEB39316 SAMEA7050465 13 ERS4811095 2021-04-11 2020-07-10 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA pch034_all WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/001/ERR4332641/ERR4332641.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/001/ERR4332641/ERR4332641.fastq.gz 240996196 27ecc647f2a82b5c1a7a36467f765d54 6722479 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332641/pch034-b1e1l1p2_AGAACCG_L005_ARmerged.180302_ST-E00269_0258_BHJF7NCCXY.all.hs37d5.fa.cons.90perc.bam +CCH285 minus ds n/a ERR4332646 PRJEB39316 SAMEA7050468 16 ERS4811098 2021-04-11 2020-07-10 Illumina NovaSeq 6000 SINGLE GENOMIC ILLUMINA CCH285_L1 WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/006/ERR4332646/ERR4332646.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/006/ERR4332646/ERR4332646.fastq.gz 184093891 d3af0bb0802d2da7d68df3cabbeb4841 4879361 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332646/CCH285-b1e1l1p1_GTTATAC-ACTTCAA_L001_ARmerged.200115_A00621_0169_BHYLNNDSXX.all.hs37d5.cons.90perc.bam +CCH294 minus ds n/a ERR4332649 PRJEB39316 SAMEA7050471 19 ERS4811101 2021-04-11 2020-07-10 Illumina NovaSeq 6000 SINGLE GENOMIC ILLUMINA CCH294_L1 WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/009/ERR4332649/ERR4332649.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/009/ERR4332649/ERR4332649.fastq.gz 610643404 6a5689763b239ff60c24bc5313892c6e 15356366 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332649/CCH294-b1e1l1p1_ACCAACG-ATTAAGG_L001_ARmerged.200115_A00621_0169_BHYLNNDSXX.all.hs37d5.cons.90perc.bam +Ash002 minus ds n/a ERR4332592 PRJEB39316 SAMEA7050404 1 ERS4811035 2021-04-11 2020-07-10 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA Ash002_all WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/002/ERR4332592/ERR4332592.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/002/ERR4332592/ERR4332592.fastq.gz 194164761 6d8831f5bb8ba9870cb55f834e98ab4d 6471092 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332592/Ash002_all.merged.hs37d5.fa.cons.90perc.bam +Ash136 minus ds n/a ERR4332632 PRJEB39316 SAMEA7050460 8 ERS4811090 2021-04-11 2020-07-10 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA Ash136_all WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/002/ERR4332632/ERR4332632.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/002/ERR4332632/ERR4332632.fastq.gz 671099104 d37d7301c8459ff7b2e737e2ccb31582 19835438 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332632/Ash136_all.merged.hs37d5.fa.cons.90perc.bam +Ash133 minus ds n/a ERR4332633 PRJEB39316 SAMEA7050459 7 ERS4811089 2021-04-11 2020-07-10 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA Ash133_all WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/003/ERR4332633/ERR4332633.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/003/ERR4332633/ERR4332633.fastq.gz 2432326317 5e401ad70be16a2e95df5fb760499cee 62454527 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332633/Ash133_all.merged.hs37d5.fa.cons.90perc.bam +cth217 minus ds n/a ERR4332634 PRJEB39316 SAMEA7050474 22 ERS4811104 2021-04-11 2020-07-10 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA cth217_all WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/004/ERR4332634/ERR4332634.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/004/ERR4332634/ERR4332634.fastq.gz 156091710 22f3a8fd26765dde15d045f3bf0f573a 4481358 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332634/cth217_all.merged.hs37d5.fa.cons.90perc.bam +cth842 minus ds n/a ERR4332640 PRJEB39316 SAMEA7050463 11 ERS4811093 2021-04-11 2020-07-10 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA cth842_all WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/000/ERR4332640/ERR4332640.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/000/ERR4332640/ERR4332640.fastq.gz 577421074 76e8349b53f62dc04d59fc09f3f31278 19618647 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332640/cth842_all.merged.hs37d5.fa.cons.90perc.bam +CCH163 minus ds n/a ERR4332645 PRJEB39316 SAMEA7050467 15 ERS4811097 2021-04-11 2020-07-10 Illumina NovaSeq 6000 SINGLE GENOMIC ILLUMINA CCH163_L1 WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/005/ERR4332645/ERR4332645.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/005/ERR4332645/ERR4332645.fastq.gz 86634518 513794058fdf06e160cad3579241fc19 2428370 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332645/CCH163-b1e1l1p1_CGTAATC-ATGGTCT_L001_ARmerged.200115_A00621_0169_BHYLNNDSXX.all.hs37d5.cons.90perc.bam +CCH289 minus ds n/a ERR4332647 PRJEB39316 SAMEA7050469 17 ERS4811099 2021-04-11 2020-07-10 Illumina NovaSeq 6000 SINGLE GENOMIC ILLUMINA CCH289_L1 WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/007/ERR4332647/ERR4332647.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/007/ERR4332647/ERR4332647.fastq.gz 179891674 a9d1316845f7c8dd6a3852a82cfc4c20 5013829 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332647/CCH289-b1e1l1p1_CTTGCGG-CTCATGG_L001_ARmerged.200115_A00621_0169_BHYLNNDSXX.all.hs37d5.cons.90perc.bam +CCH290 minus ds n/a ERR4332648 PRJEB39316 SAMEA7050470 18 ERS4811100 2021-04-11 2020-07-10 Illumina NovaSeq 6000 SINGLE GENOMIC ILLUMINA CCH290_L1 WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/008/ERR4332648/ERR4332648.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/008/ERR4332648/ERR4332648.fastq.gz 30401831 352d76ddb75edee7e30ba0800940b126 765274 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332648/CCH290-b1e1l1p1_AATCTTC-TGATAGT_L001_ARmerged.200115_A00621_0169_BHYLNNDSXX.all.hs37d5.cons.90perc.bam +Ash033 minus ds n/a ERR4331996 PRJEB39316 SAMEA7050454 2 ERS4811084 2021-04-11 2020-07-09 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA Ash033_all WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/006/ERR4331996/ERR4331996.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/006/ERR4331996/ERR4331996.fastq.gz 649563861 9bd0fceb5ab46cb894ea33765c122e83 23386349 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4331996/Ash033_all.merged.hs37d5.fa.cons.90perc.bam +Ash040 minus ds n/a ERR4332593 PRJEB39316 SAMEA7050455 3 ERS4811085 2021-04-11 2020-07-10 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA Ash040_all WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/003/ERR4332593/ERR4332593.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/003/ERR4332593/ERR4332593.fastq.gz 276693447 539852f3d7fb574b2a1e4f1c0059f163 9442394 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332593/Ash040_all.merged.hs37d5.fa.cons.90perc.bam +Ash129 minus ds n/a ERR4332594 PRJEB39316 SAMEA7050457 5 ERS4811087 2021-04-11 2020-07-10 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA Ash129_all WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/004/ERR4332594/ERR4332594.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/004/ERR4332594/ERR4332594.fastq.gz 2503643788 4991d0030214687c7c1706c640a2b37e 76891816 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332594/Ash129_all.merged.hs37d5.fa.cons.90perc.bam +Ash131 minus ds n/a ERR4332631 PRJEB39316 SAMEA7050458 6 ERS4811088 2021-04-11 2020-07-10 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA Ash131_all WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/001/ERR4332631/ERR4332631.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/001/ERR4332631/ERR4332631.fastq.gz 535696334 3c680096683defd93b35a5f4004e9e87 16781594 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332631/Ash131_all.merged.hs37d5.fa.cons.90perc.bam +cth006 minus ds n/a ERR4332635 PRJEB39316 SAMEA7050461 9 ERS4811091 2021-04-11 2020-07-10 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA cth006_all WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/005/ERR4332635/ERR4332635.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/005/ERR4332635/ERR4332635.fastq.gz 505068759 685f3c0aafd9a74b1b71e6c14dae8f1c 16351320 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332635/cth006_all.merged.hs37d5.fa.cons.90perc.bam +cth728 minus ds n/a ERR4332636 PRJEB39316 SAMEA7050462 10 ERS4811092 2021-04-11 2020-07-10 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA cth728_all WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/006/ERR4332636/ERR4332636.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/006/ERR4332636/ERR4332636.fastq.gz 221723438 3f23731850c9e48012bd71d4ccc773cd 6209127 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332636/cth728_all.merged.hs37d5.fa.cons.90perc.bam +cth747 minus ds n/a ERR4332638 PRJEB39316 SAMEA7050464 12 ERS4811094 2021-04-11 2020-07-10 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA cth747_all WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/008/ERR4332638/ERR4332638.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/008/ERR4332638/ERR4332638.fastq.gz 604529786 a1a37e278ea0e4632e2a0d43adbaa79c 18850253 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332638/cth747_all.merged.hs37d5.fa.cons.90perc.bam +cth739 minus ds n/a ERR4332639 PRJEB39316 SAMEA7050473 21 ERS4811103 2021-04-11 2020-07-10 Illumina HiSeq 2500 SINGLE GENOMIC ILLUMINA cth739_all WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/009/ERR4332639/ERR4332639.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/009/ERR4332639/ERR4332639.fastq.gz 1315991788 424b8c541b55c1cbef84028ac8b6be70 45491923 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332639/cth739_all.merged.hs37d5.fa.cons.90perc.bam +CCH144 minus ds n/a ERR4332643 PRJEB39316 SAMEA7050466 14 ERS4811096 2021-04-11 2020-07-10 Illumina NovaSeq 6000 SINGLE GENOMIC ILLUMINA CCH144_L1 WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/003/ERR4332643/ERR4332643.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/003/ERR4332643/ERR4332643.fastq.gz 152189811 9d88cd959221c96105afbcb6bb0fb07f 4212571 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332643/CCH144-b1e1l1p1_TACTTAG-GTCAACC_L001_ARmerged.200115_A00621_0169_BHYLNNDSXX.all.hs37d5.cons.90perc.bam +CCH311 minus ds n/a ERR4332650 PRJEB39316 SAMEA7050472 20 ERS4811102 2021-04-11 2020-07-10 Illumina NovaSeq 6000 SINGLE GENOMIC ILLUMINA CCH311_L1 WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/000/ERR4332650/ERR4332650.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/000/ERR4332650/ERR4332650.fastq.gz 308098723 b67b26467df5117d6269793a9a63349e 7539845 ftp.sra.ebi.ac.uk/vol1/run/ERR433/ERR4332650/CCH311-b1e1l1p1_AACCATG-CTACTCT_L001_ARmerged.200115_A00621_0169_BHYLNNDSXX.all.hs37d5.cons.90perc.bam From 23c26aef600ca36022db6ad48e62d2ca833b4d8a Mon Sep 17 00:00:00 2001 From: delphis-bot Date: Tue, 25 Jul 2023 13:53:05 +0000 Subject: [PATCH 5/6] [automated] Create processing backbone from SSF files --- .../2020_Nagele_Caribbean.config | 39 ++++ .../2020_Nagele_Caribbean.tsv | 185 ++++++++++++++++++ .../2020_Nagele_Caribbean.tsv_patch.sh | 45 +++++ .../2020_Nagele_Caribbean/script_versions.txt | 2 + 4 files changed, 271 insertions(+) create mode 100644 packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.config create mode 100644 packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.tsv create mode 100755 packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.tsv_patch.sh create mode 100644 packages/2020_Nagele_Caribbean/script_versions.txt diff --git a/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.config b/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.config new file mode 100644 index 0000000..1b03016 --- /dev/null +++ b/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.config @@ -0,0 +1,39 @@ +// Keep track of config versions +config_template_version='0.2.0dev' +package_config_version='0.2.0dev' + +// This configuration file is designed to be a used with the nf-core/eager pipeline. +// Instead of having to specify all other configurations for the Minotaur pipeline +// on runtime, they are all contained in this file and loaded automatically upon +// specifying this config file during runtime. Additionally, any parameters that +// need to be altered from the defaults can be specified here. +// +// The intention is to make it easy for users to understand and reproduce the output +// from processing with the Minotaur workflow processing from the contents of a +// single file. + +// Load configuration profiles +includeConfig "../../conf/EVA_cluster.config" // Cluster-specific configurations for nf-core/eager execution at MPI-EVA +includeConfig "../../conf/Minotaur.config" // Default nf-core/eager parameters for Minotaur processing. + +// The following config file specifies BED files for on-target endogenous DNA calculation and mean coverage as well as pseudohaploid genotyping. +// TODO: Select the appropriate config for the CaptureType of the package. +includeConfig '../../conf/CaptureType_profiles/1240K.config' + +params { + // Keep track of config file versions used when processing + config_profile_description = "${config_profile_description}\nconfig_template_version: ${config_template_version}\npackage_config_version: ${package_config_version}" + config_profile_contact = "Thiseas C. Lamnidis (@TCLamnidis)" + + /* + TODO: If you need to change any of the default processing parameters for this package + you can specify these parameters below. + Any parameters not specified in any of the config files default to their nf-core/eager default values. + + For information on all available parameters and their default values see: + https://nf-co.re/eager/2.4.6/parameters + + You can see the default values for parameters within poseidon-eager at: + https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Minotaur.config + */ +} diff --git a/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.tsv b/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.tsv new file mode 100644 index 0000000..a2fe6a2 --- /dev/null +++ b/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.tsv @@ -0,0 +1,185 @@ +Sample_Name Library_ID Lane Colour_Chemistry SeqType Organism Strandedness UDG_Treatment R1 R2 BAM R1_target_file R2_target_file +ALG002 ALG002_ALG002.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double none /ALG002_ALG002.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170303.fastq.gz NA +ALG003 ALG003_ALG003.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double none /ALG003_ALG003.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170304.fastq.gz NA +CAO002008 CAO002008_CAO002008.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO002008_CAO002008.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170309.fastq.gz NA +CAO006 CAO006_CAO006.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO006_CAO006.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170311.fastq.gz NA +CAO007 CAO007_CAO007.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO007_CAO007.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170312.fastq.gz NA +CAO012 CAO012_CAO012.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO012_CAO012.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170316.fastq.gz NA +CAO015 CAO015_CAO015.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO015_CAO015.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170318.fastq.gz NA +CAO022026 CAO022026_CAO022026.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO022026_CAO022026.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170325.fastq.gz NA +CAO027 CAO027_CAO027.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO027_CAO027.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170328.fastq.gz NA +CAO030 CAO030_CAO030.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO030_CAO030.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170331.fastq.gz NA +CAO031 CAO031_CAO031.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO031_CAO031.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170332.fastq.gz NA +CDE001 CDE001_CDE001.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CDE001_CDE001.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170334.fastq.gz NA +CDE005 CDE005_CDE005.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CDE005_CDE005.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170338.fastq.gz NA +CIP001 CIP001_CIP001.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /CIP001_CIP001.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170339.fastq.gz NA +CIP003 CIP003_CIP003.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /CIP003_CIP003.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170341.fastq.gz NA +CIP008 CIP008_CIP008.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /CIP008_CIP008.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170343.fastq.gz NA +CIP009 CIP009_CIP009.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /CIP009_CIP009.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170344.fastq.gz NA +CIP011 CIP011_CIP011.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /CIP011_CIP011.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170346.fastq.gz NA +ELM001 ELM001_ELM001.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /ELM001_ELM001.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170351.fastq.gz NA +GUY002 GUY002_GUY002.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /GUY002_GUY002.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170353.fastq.gz NA +LAV006 LAV006_LAV006.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /LAV006_LAV006.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170360.fastq.gz NA +PCA002 PCA002_PCA002.A0101.TF1.1.1 1 4 SE Homo sapiens (modern human) double half /PCA002_PCA002.A0101.TF1.1.1_L1_R1.fastq.gz NA NA ERR4170370.fastq.gz NA +PCA009 PCA009_PCA009.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /PCA009_PCA009.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170372.fastq.gz NA +PDI003 PDI003_PDI003.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /PDI003_PDI003.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170378.fastq.gz NA +PDI010 PDI010_PDI010.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /PDI010_PDI010.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170382.fastq.gz NA +PDI011 PDI011_PDI011.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /PDI011_PDI011.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170383.fastq.gz NA +PDM001 PDM001_PDM001.A0101.TF12.12 1 4 SE Homo sapiens (modern human) double half /PDM001_PDM001.A0101.TF12.12_L1_R1.fastq.gz NA NA ERR4170385.fastq.gz NA +PDM002 PDM002_PDM002.A0101.TF12.12 1 4 SE Homo sapiens (modern human) double half /PDM002_PDM002.A0101.TF12.12_L1_R1.fastq.gz NA NA ERR4170386.fastq.gz NA +PDM008 PDM008_PDM008.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /PDM008_PDM008.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170390.fastq.gz NA +TIB002 TIB002_TIB002.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /TIB002_TIB002.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170394.fastq.gz NA +ALG002 ALG002_ALG002.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double none /ALG002_ALG002.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170396.fastq.gz NA +CAO001 CAO001_CAO001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO001_CAO001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170401.fastq.gz NA +CAO002008 CAO002008_CAO002008.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO002008_CAO002008.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170402.fastq.gz NA +CAO007 CAO007_CAO007.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO007_CAO007.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170405.fastq.gz NA +CAO010 CAO010_CAO010.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO010_CAO010.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170407.fastq.gz NA +CAO015 CAO015_CAO015.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO015_CAO015.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170411.fastq.gz NA +CAO019 CAO019_CAO019.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO019_CAO019.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170415.fastq.gz NA +CAO021 CAO021_CAO021.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO021_CAO021.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170417.fastq.gz NA +CAO024 CAO024_CAO024.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO024_CAO024.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170420.fastq.gz NA +CAO029 CAO029_CAO029.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO029_CAO029.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170423.fastq.gz NA +CAO031 CAO031_CAO031.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO031_CAO031.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170425.fastq.gz NA +CIP002 CIP002_CIP002.A0101.MT1.12 1 4 SE Homo sapiens (modern human) double half /CIP002_CIP002.A0101.MT1.12_L1_R1.fastq.gz NA NA ERR4170433.fastq.gz NA +CIP003 CIP003_CIP003.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CIP003_CIP003.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170434.fastq.gz NA +CIP007012 CIP007012_CIP007012.A0101.MT1.12 1 4 SE Homo sapiens (modern human) double half /CIP007012_CIP007012.A0101.MT1.12_L1_R1.fastq.gz NA NA ERR4170435.fastq.gz NA +CUC002 CUC002_CUC002.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CUC002_CUC002.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170441.fastq.gz NA +LAV001 LAV001_LAV001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /LAV001_LAV001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170448.fastq.gz NA +LAV006 LAV006_LAV006.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /LAV006_LAV006.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170453.fastq.gz NA +LAV007 LAV007_LAV007.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /LAV007_LAV007.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170454.fastq.gz NA +LAV008 LAV008_LAV008.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /LAV008_LAV008.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170455.fastq.gz NA +LAV010 LAV010_LAV010.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /LAV010_LAV010.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170457.fastq.gz NA +LAV011 LAV011_LAV011.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /LAV011_LAV011.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170458.fastq.gz NA +LOI001 LOI001_LOI001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /LOI001_LOI001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170460.fastq.gz NA +PCA001 PCA001_PCA001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PCA001_PCA001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170462.fastq.gz NA +PCA002 PCA002_PCA002.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PCA002_PCA002.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170463.fastq.gz NA +PCV003 PCV003_PCV003.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PCV003_PCV003.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170469.fastq.gz NA +PCV004 PCV004_PCV004.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PCV004_PCV004.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170470.fastq.gz NA +PDI003 PDI003_PDI003.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PDI003_PDI003.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170471.fastq.gz NA +PDI008 PDI008_PDI008.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PDI008_PDI008.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170473.fastq.gz NA +PDM001 PDM001_PDM001.A0101.MT1.12 1 4 SE Homo sapiens (modern human) double half /PDM001_PDM001.A0101.MT1.12_L1_R1.fastq.gz NA NA ERR4170478.fastq.gz NA +PDM003 PDM003_PDM003.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PDM003_PDM003.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170480.fastq.gz NA +PDM004 PDM004_PDM004.B0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PDM004_PDM004.B0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170481.fastq.gz NA +PDM006 PDM006_PDM006.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PDM006_PDM006.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170482.fastq.gz NA +TIB002 TIB002_TIB002.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /TIB002_TIB002.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170487.fastq.gz NA +ALG001 ALG001_ALG001.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double none /ALG001_ALG001.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170302.fastq.gz NA +CAA001003 CAA001003_CAA001003.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /CAA001003_CAA001003.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170306.fastq.gz NA +CAO017 CAO017_CAO017.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO017_CAO017.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170320.fastq.gz NA +CAO019 CAO019_CAO019.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO019_CAO019.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170322.fastq.gz NA +CAO020 CAO020_CAO020.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO020_CAO020.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170323.fastq.gz NA +CAO024 CAO024_CAO024.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO024_CAO024.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170327.fastq.gz NA +CAO028 CAO028_CAO028.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO028_CAO028.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170329.fastq.gz NA +CAO029 CAO029_CAO029.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO029_CAO029.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170330.fastq.gz NA +CDE002 CDE002_CDE002.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CDE002_CDE002.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170335.fastq.gz NA +CDE004 CDE004_CDE004.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CDE004_CDE004.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170337.fastq.gz NA +CIP010 CIP010_CIP010.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /CIP010_CIP010.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170345.fastq.gz NA +CUC002 CUC002_CUC002.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CUC002_CUC002.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170348.fastq.gz NA +CUC003 CUC003_CUC003.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CUC003_CUC003.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170349.fastq.gz NA +CUC004 CUC004_CUC004.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CUC004_CUC004.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170350.fastq.gz NA +GUY001 GUY001_GUY001.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /GUY001_GUY001.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170352.fastq.gz NA +LAV005 LAV005_LAV005.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /LAV005_LAV005.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170359.fastq.gz NA +LAV012 LAV012_LAV012.A0101.TF1.1.1 1 4 SE Homo sapiens (modern human) double half /LAV012_LAV012.A0101.TF1.1.1_L1_R1.fastq.gz NA NA ERR4170366.fastq.gz NA +MTO001 MTO001_MTO001.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /MTO001_MTO001.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170368.fastq.gz NA +PCA006 PCA006_PCA006.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /PCA006_PCA006.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170371.fastq.gz NA +PCA010 PCA010_PCA010.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /PCA010_PCA010.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170373.fastq.gz NA +PDI006 PDI006_PDI006.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /PDI006_PDI006.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170379.fastq.gz NA +PDI008 PDI008_PDI008.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /PDI008_PDI008.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170380.fastq.gz NA +PDI012013 PDI012013_PDI012013.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /PDI012013_PDI012013.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170384.fastq.gz NA +PDM006 PDM006_PDM006.A0101.TF2.1 1 4 SE Homo sapiens (modern human) double half /PDM006_PDM006.A0101.TF2.1_L1_R1.fastq.gz NA NA ERR4170389.fastq.gz NA +PDM010 PDM010_PDM010.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /PDM010_PDM010.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170392.fastq.gz NA +ALG003 ALG003_ALG003.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double none /ALG003_ALG003.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170397.fastq.gz NA +ALG004 ALG004_ALG004.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double none /ALG004_ALG004.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170398.fastq.gz NA +CAA001003 CAA001003_CAA001003.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAA001003_CAA001003.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170399.fastq.gz NA +CAO009013 CAO009013_CAO009013.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO009013_CAO009013.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170406.fastq.gz NA +CAO014 CAO014_CAO014.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO014_CAO014.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170410.fastq.gz NA +CAO016 CAO016_CAO016.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO016_CAO016.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170412.fastq.gz NA +CAO018 CAO018_CAO018.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO018_CAO018.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170414.fastq.gz NA +CAO022026 CAO022026_CAO022026.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO022026_CAO022026.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170418.fastq.gz NA +CAO023025 CAO023025_CAO023025.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO023025_CAO023025.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170419.fastq.gz NA +CAO030 CAO030_CAO030.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO030_CAO030.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170424.fastq.gz NA +CAO032 CAO032_CAO032.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO032_CAO032.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170426.fastq.gz NA +CDE001 CDE001_CDE001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CDE001_CDE001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170427.fastq.gz NA +CDE002 CDE002_CDE002.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CDE002_CDE002.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170428.fastq.gz NA +CDE003 CDE003_CDE003.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CDE003_CDE003.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170429.fastq.gz NA +CDE005 CDE005_CDE005.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CDE005_CDE005.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170431.fastq.gz NA +CIP001 CIP001_CIP001.A0101.TF1.1mt 1 4 SE Homo sapiens (modern human) double half /CIP001_CIP001.A0101.TF1.1mt_L1_R1.fastq.gz NA NA ERR4170432.fastq.gz NA +CIP009 CIP009_CIP009.A0101.MT1.12 1 4 SE Homo sapiens (modern human) double half /CIP009_CIP009.A0101.MT1.12_L1_R1.fastq.gz NA NA ERR4170437.fastq.gz NA +CUC001 CUC001_CUC001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CUC001_CUC001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170440.fastq.gz NA +CUC003 CUC003_CUC003.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CUC003_CUC003.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170442.fastq.gz NA +GUY002 GUY002_GUY002.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /GUY002_GUY002.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170446.fastq.gz NA +LAV002 LAV002_LAV002.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /LAV002_LAV002.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170449.fastq.gz NA +LAV003 LAV003_LAV003.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /LAV003_LAV003.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170450.fastq.gz NA +LAV005 LAV005_LAV005.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /LAV005_LAV005.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170452.fastq.gz NA +LAV009 LAV009_LAV009.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /LAV009_LAV009.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170456.fastq.gz NA +LAV012 LAV012_LAV012.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /LAV012_LAV012.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170459.fastq.gz NA +MTO001 MTO001_MTO001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /MTO001_MTO001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170461.fastq.gz NA +PCA006 PCA006_PCA006.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PCA006_PCA006.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170464.fastq.gz NA +PCA010 PCA010_PCA010.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PCA010_PCA010.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170466.fastq.gz NA +PDI006 PDI006_PDI006.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PDI006_PDI006.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170472.fastq.gz NA +PDI010 PDI010_PDI010.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PDI010_PDI010.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170475.fastq.gz NA +PDI011 PDI011_PDI011.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PDI011_PDI011.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170476.fastq.gz NA +PDM002 PDM002_PDM002.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PDM002_PDM002.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170479.fastq.gz NA +TIB001 TIB001_TIB001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /TIB001_TIB001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170486.fastq.gz NA +ALG004 ALG004_ALG004.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double none /ALG004_ALG004.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170305.fastq.gz NA +CAO001 CAO001_CAO001.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO001_CAO001.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170308.fastq.gz NA +CAO004 CAO004_CAO004.B0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO004_CAO004.B0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170310.fastq.gz NA +CAO009013 CAO009013_CAO009013.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO009013_CAO009013.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170313.fastq.gz NA +CAO010 CAO010_CAO010.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO010_CAO010.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170314.fastq.gz NA +CAO011 CAO011_CAO011.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO011_CAO011.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170315.fastq.gz NA +CAO014 CAO014_CAO014.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO014_CAO014.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170317.fastq.gz NA +CAO016 CAO016_CAO016.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO016_CAO016.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170319.fastq.gz NA +CAO018 CAO018_CAO018.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO018_CAO018.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170321.fastq.gz NA +CAO021 CAO021_CAO021.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO021_CAO021.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170324.fastq.gz NA +CAO023025 CAO023025_CAO023025.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO023025_CAO023025.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170326.fastq.gz NA +CAO032 CAO032_CAO032.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CAO032_CAO032.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170333.fastq.gz NA +CDE003 CDE003_CDE003.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CDE003_CDE003.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170336.fastq.gz NA +CIP002 CIP002_CIP002.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /CIP002_CIP002.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170340.fastq.gz NA +CIP007012 CIP007012_CIP007012.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /CIP007012_CIP007012.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170342.fastq.gz NA +CUC001 CUC001_CUC001.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /CUC001_CUC001.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170347.fastq.gz NA +GUY003 GUY003_GUY003.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /GUY003_GUY003.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170354.fastq.gz NA +LAV001 LAV001_LAV001.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /LAV001_LAV001.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170355.fastq.gz NA +LAV002 LAV002_LAV002.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /LAV002_LAV002.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170356.fastq.gz NA +LAV003 LAV003_LAV003.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /LAV003_LAV003.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170357.fastq.gz NA +LAV004 LAV004_LAV004.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /LAV004_LAV004.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170358.fastq.gz NA +LAV007 LAV007_LAV007.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /LAV007_LAV007.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170361.fastq.gz NA +LAV008 LAV008_LAV008.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /LAV008_LAV008.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170362.fastq.gz NA +LAV009 LAV009_LAV009.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /LAV009_LAV009.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170363.fastq.gz NA +LAV010 LAV010_LAV010.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /LAV010_LAV010.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170364.fastq.gz NA +LAV011 LAV011_LAV011.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /LAV011_LAV011.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170365.fastq.gz NA +LOI001 LOI001_LOI001.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /LOI001_LOI001.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170367.fastq.gz NA +PCA001 PCA001_PCA001.A0101.TF1.1.1 1 4 SE Homo sapiens (modern human) double half /PCA001_PCA001.A0101.TF1.1.1_L1_R1.fastq.gz NA NA ERR4170369.fastq.gz NA +PCV001 PCV001_PCV001.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /PCV001_PCV001.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170374.fastq.gz NA +PCV002 PCV002_PCV002.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /PCV002_PCV002.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170375.fastq.gz NA +PCV003 PCV003_PCV003.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /PCV003_PCV003.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170376.fastq.gz NA +PCV004 PCV004_PCV004.A0101.TF1.12 1 4 SE Homo sapiens (modern human) double half /PCV004_PCV004.A0101.TF1.12_L1_R1.fastq.gz NA NA ERR4170377.fastq.gz NA +PDI009 PDI009_PDI009.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /PDI009_PDI009.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170381.fastq.gz NA +PDM003 PDM003_PDM003.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /PDM003_PDM003.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170387.fastq.gz NA +PDM004 PDM004_PDM004.B0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /PDM004_PDM004.B0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170388.fastq.gz NA +PDM009 PDM009_PDM009.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /PDM009_PDM009.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170391.fastq.gz NA +TIB001 TIB001_TIB001.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half /TIB001_TIB001.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR4170393.fastq.gz NA +ALG001 ALG001_ALG001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double none /ALG001_ALG001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170395.fastq.gz NA +CAO004 CAO004_CAO004.B0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO004_CAO004.B0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170403.fastq.gz NA +CAO006 CAO006_CAO006.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO006_CAO006.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170404.fastq.gz NA +CAO011 CAO011_CAO011.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO011_CAO011.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170408.fastq.gz NA +CAO012 CAO012_CAO012.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO012_CAO012.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170409.fastq.gz NA +CAO017 CAO017_CAO017.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO017_CAO017.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170413.fastq.gz NA +CAO020 CAO020_CAO020.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO020_CAO020.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170416.fastq.gz NA +CAO027 CAO027_CAO027.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO027_CAO027.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170421.fastq.gz NA +CAO028 CAO028_CAO028.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CAO028_CAO028.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170422.fastq.gz NA +CDE004 CDE004_CDE004.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CDE004_CDE004.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170430.fastq.gz NA +CIP008 CIP008_CIP008.A0101.MT1.12 1 4 SE Homo sapiens (modern human) double half /CIP008_CIP008.A0101.MT1.12_L1_R1.fastq.gz NA NA ERR4170436.fastq.gz NA +CIP010 CIP010_CIP010.A0101.MT1.12 1 4 SE Homo sapiens (modern human) double half /CIP010_CIP010.A0101.MT1.12_L1_R1.fastq.gz NA NA ERR4170438.fastq.gz NA +CIP011 CIP011_CIP011.A0101.MT1.12 1 4 SE Homo sapiens (modern human) double half /CIP011_CIP011.A0101.MT1.12_L1_R1.fastq.gz NA NA ERR4170439.fastq.gz NA +CUC004 CUC004_CUC004.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /CUC004_CUC004.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170443.fastq.gz NA +ELM001 ELM001_ELM001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /ELM001_ELM001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170444.fastq.gz NA +GUY001 GUY001_GUY001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /GUY001_GUY001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170445.fastq.gz NA +GUY003 GUY003_GUY003.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /GUY003_GUY003.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170447.fastq.gz NA +LAV004 LAV004_LAV004.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /LAV004_LAV004.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170451.fastq.gz NA +PCA009 PCA009_PCA009.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PCA009_PCA009.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170465.fastq.gz NA +PCV001 PCV001_PCV001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PCV001_PCV001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170467.fastq.gz NA +PCV002 PCV002_PCV002.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PCV002_PCV002.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170468.fastq.gz NA +PDI009 PDI009_PDI009.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PDI009_PDI009.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170474.fastq.gz NA +PDI012013 PDI012013_PDI012013.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PDI012013_PDI012013.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170477.fastq.gz NA +PDM008 PDM008_PDM008.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PDM008_PDM008.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170483.fastq.gz NA +PDM009 PDM009_PDM009.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PDM009_PDM009.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170484.fastq.gz NA +PDM010 PDM010_PDM010.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half /PDM010_PDM010.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR4170485.fastq.gz NA diff --git a/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.tsv_patch.sh b/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.tsv_patch.sh new file mode 100755 index 0000000..422e836 --- /dev/null +++ b/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.tsv_patch.sh @@ -0,0 +1,45 @@ +#!/usr/bin/env bash +set -uo pipefail ## Pipefail, complain on new unassigned variables. + +## Track the version of the TSV_patch template used +VERSION='0.2.0dev' + +## This script is applied to the eager input TSV file locally to edit the dummy +## path to the fastQ files added by `create_eager_input.sh` to a real local +## path provided as a positional argument. Any further local tweaks to the +## TSV before running eager should be added below that in the form of bash +## commands to aid in reproducibility. + +## usage tsv_patch.sh + +local_data_dir="$(readlink -f ${1})" +input_tsv="$(readlink -f ${2})" +output_tsv="$(dirname ${local_data_dir})/$(basename -s ".tsv" ${input_tsv}).finalised.tsv" +columns_to_keep=("Sample_Name" "Library_ID" "Lane" "Colour_Chemistry" "SeqType" "Organism" "Strandedness" "UDG_Treatment" "R1" "R2" "BAM") +source $(dirname ${2})/../../scripts/source_me.sh ## Load helper functions + +## Index non-proliferated columns and exclude them from the finalised TSV +cut_selector='' +tsv_header=($(head -n1 ${input_tsv})) +for col_name in ${columns_to_keep[@]}; do + let idx=$(get_index_of ${col_name} "${columns_to_keep[@]}")+1 ## awk uses 1-based indexing + if [[ ! ${idx} -eq -1 ]]; then + cut_selector+="${idx}," + fi +done + +## Remove added columns, and put columns in right order +cut -f ${cut_selector%,} ${input_tsv} > ${output_tsv} +sed -i -e "s||${local_data_dir}|g" ${output_tsv} + +## Any further commands to edit the file before finalisation should be added below as shown +# sed -ie 's/replace_this/with_this/g' ${output_tsv} + +## Keep track of versions +version_file="$(dirname ${input_tsv})/script_versions.txt" +## Remove versions from older run if there +grep -v -F -e "$(basename ${0})" -e "source_me.sh for final TSV" ${version_file} >${version_file}.new +## Then add new versions +echo -e "$(basename ${0}):\t${VERSION}" >> ${version_file}.new +echo -e "source_me.sh for final TSV:\t${HELPER_FUNCTION_VERSION}" >>${version_file}.new +mv ${version_file}.new ${version_file} diff --git a/packages/2020_Nagele_Caribbean/script_versions.txt b/packages/2020_Nagele_Caribbean/script_versions.txt new file mode 100644 index 0000000..be6857b --- /dev/null +++ b/packages/2020_Nagele_Caribbean/script_versions.txt @@ -0,0 +1,2 @@ +create_eager_input.sh: 0.2.1dev +source_me.sh for initial TSV: 0.2.1dev From c72f0e86b9176227720a517cfded0b87920667c6 Mon Sep 17 00:00:00 2001 From: delphis-bot Date: Tue, 25 Jul 2023 13:53:06 +0000 Subject: [PATCH 6/6] [automated] Create processing backbone from SSF files --- .../2021_Yaka_Anatolia.config | 39 ++++++++++++++++ .../2021_Yaka_Anatolia/2021_Yaka_Anatolia.tsv | 23 ++++++++++ .../2021_Yaka_Anatolia.tsv_patch.sh | 45 +++++++++++++++++++ .../2021_Yaka_Anatolia/script_versions.txt | 2 + 4 files changed, 109 insertions(+) create mode 100644 packages/2021_Yaka_Anatolia/2021_Yaka_Anatolia.config create mode 100644 packages/2021_Yaka_Anatolia/2021_Yaka_Anatolia.tsv create mode 100755 packages/2021_Yaka_Anatolia/2021_Yaka_Anatolia.tsv_patch.sh create mode 100644 packages/2021_Yaka_Anatolia/script_versions.txt diff --git a/packages/2021_Yaka_Anatolia/2021_Yaka_Anatolia.config b/packages/2021_Yaka_Anatolia/2021_Yaka_Anatolia.config new file mode 100644 index 0000000..1b03016 --- /dev/null +++ b/packages/2021_Yaka_Anatolia/2021_Yaka_Anatolia.config @@ -0,0 +1,39 @@ +// Keep track of config versions +config_template_version='0.2.0dev' +package_config_version='0.2.0dev' + +// This configuration file is designed to be a used with the nf-core/eager pipeline. +// Instead of having to specify all other configurations for the Minotaur pipeline +// on runtime, they are all contained in this file and loaded automatically upon +// specifying this config file during runtime. Additionally, any parameters that +// need to be altered from the defaults can be specified here. +// +// The intention is to make it easy for users to understand and reproduce the output +// from processing with the Minotaur workflow processing from the contents of a +// single file. + +// Load configuration profiles +includeConfig "../../conf/EVA_cluster.config" // Cluster-specific configurations for nf-core/eager execution at MPI-EVA +includeConfig "../../conf/Minotaur.config" // Default nf-core/eager parameters for Minotaur processing. + +// The following config file specifies BED files for on-target endogenous DNA calculation and mean coverage as well as pseudohaploid genotyping. +// TODO: Select the appropriate config for the CaptureType of the package. +includeConfig '../../conf/CaptureType_profiles/1240K.config' + +params { + // Keep track of config file versions used when processing + config_profile_description = "${config_profile_description}\nconfig_template_version: ${config_template_version}\npackage_config_version: ${package_config_version}" + config_profile_contact = "Thiseas C. Lamnidis (@TCLamnidis)" + + /* + TODO: If you need to change any of the default processing parameters for this package + you can specify these parameters below. + Any parameters not specified in any of the config files default to their nf-core/eager default values. + + For information on all available parameters and their default values see: + https://nf-co.re/eager/2.4.6/parameters + + You can see the default values for parameters within poseidon-eager at: + https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Minotaur.config + */ +} diff --git a/packages/2021_Yaka_Anatolia/2021_Yaka_Anatolia.tsv b/packages/2021_Yaka_Anatolia/2021_Yaka_Anatolia.tsv new file mode 100644 index 0000000..e2801a4 --- /dev/null +++ b/packages/2021_Yaka_Anatolia/2021_Yaka_Anatolia.tsv @@ -0,0 +1,23 @@ +Sample_Name Library_ID Lane Colour_Chemistry SeqType Organism Strandedness UDG_Treatment R1 R2 BAM R1_target_file R2_target_file +Ash128 Ash128_Ash128_all 1 4 SE Homo sapiens (modern human) double none /Ash128_Ash128_all_L1_R1.fastq.gz NA NA ERR4332637.fastq.gz NA +pch034 pch034_pch034_all 1 4 SE Homo sapiens (modern human) double none /pch034_pch034_all_L1_R1.fastq.gz NA NA ERR4332641.fastq.gz NA +CCH285 CCH285_CCH285_L1 1 4 SE Homo sapiens (modern human) double none /CCH285_CCH285_L1_L1_R1.fastq.gz NA NA ERR4332646.fastq.gz NA +CCH294 CCH294_CCH294_L1 1 4 SE Homo sapiens (modern human) double none /CCH294_CCH294_L1_L1_R1.fastq.gz NA NA ERR4332649.fastq.gz NA +Ash002 Ash002_Ash002_all 1 4 SE Homo sapiens (modern human) double none /Ash002_Ash002_all_L1_R1.fastq.gz NA NA ERR4332592.fastq.gz NA +Ash136 Ash136_Ash136_all 1 4 SE Homo sapiens (modern human) double none /Ash136_Ash136_all_L1_R1.fastq.gz NA NA ERR4332632.fastq.gz NA +Ash133 Ash133_Ash133_all 1 4 SE Homo sapiens (modern human) double none /Ash133_Ash133_all_L1_R1.fastq.gz NA NA ERR4332633.fastq.gz NA +cth217 cth217_cth217_all 1 4 SE Homo sapiens (modern human) double none /cth217_cth217_all_L1_R1.fastq.gz NA NA ERR4332634.fastq.gz NA +cth842 cth842_cth842_all 1 4 SE Homo sapiens (modern human) double none /cth842_cth842_all_L1_R1.fastq.gz NA NA ERR4332640.fastq.gz NA +CCH163 CCH163_CCH163_L1 1 4 SE Homo sapiens (modern human) double none /CCH163_CCH163_L1_L1_R1.fastq.gz NA NA ERR4332645.fastq.gz NA +CCH289 CCH289_CCH289_L1 1 4 SE Homo sapiens (modern human) double none /CCH289_CCH289_L1_L1_R1.fastq.gz NA NA ERR4332647.fastq.gz NA +CCH290 CCH290_CCH290_L1 1 4 SE Homo sapiens (modern human) double none /CCH290_CCH290_L1_L1_R1.fastq.gz NA NA ERR4332648.fastq.gz NA +Ash033 Ash033_Ash033_all 1 4 SE Homo sapiens (modern human) double none /Ash033_Ash033_all_L1_R1.fastq.gz NA NA ERR4331996.fastq.gz NA +Ash040 Ash040_Ash040_all 1 4 SE Homo sapiens (modern human) double none /Ash040_Ash040_all_L1_R1.fastq.gz NA NA ERR4332593.fastq.gz NA +Ash129 Ash129_Ash129_all 1 4 SE Homo sapiens (modern human) double none /Ash129_Ash129_all_L1_R1.fastq.gz NA NA ERR4332594.fastq.gz NA +Ash131 Ash131_Ash131_all 1 4 SE Homo sapiens (modern human) double none /Ash131_Ash131_all_L1_R1.fastq.gz NA NA ERR4332631.fastq.gz NA +cth006 cth006_cth006_all 1 4 SE Homo sapiens (modern human) double none /cth006_cth006_all_L1_R1.fastq.gz NA NA ERR4332635.fastq.gz NA +cth728 cth728_cth728_all 1 4 SE Homo sapiens (modern human) double none /cth728_cth728_all_L1_R1.fastq.gz NA NA ERR4332636.fastq.gz NA +cth747 cth747_cth747_all 1 4 SE Homo sapiens (modern human) double none /cth747_cth747_all_L1_R1.fastq.gz NA NA ERR4332638.fastq.gz NA +cth739 cth739_cth739_all 1 4 SE Homo sapiens (modern human) double none /cth739_cth739_all_L1_R1.fastq.gz NA NA ERR4332639.fastq.gz NA +CCH144 CCH144_CCH144_L1 1 4 SE Homo sapiens (modern human) double none /CCH144_CCH144_L1_L1_R1.fastq.gz NA NA ERR4332643.fastq.gz NA +CCH311 CCH311_CCH311_L1 1 4 SE Homo sapiens (modern human) double none /CCH311_CCH311_L1_L1_R1.fastq.gz NA NA ERR4332650.fastq.gz NA diff --git a/packages/2021_Yaka_Anatolia/2021_Yaka_Anatolia.tsv_patch.sh b/packages/2021_Yaka_Anatolia/2021_Yaka_Anatolia.tsv_patch.sh new file mode 100755 index 0000000..422e836 --- /dev/null +++ b/packages/2021_Yaka_Anatolia/2021_Yaka_Anatolia.tsv_patch.sh @@ -0,0 +1,45 @@ +#!/usr/bin/env bash +set -uo pipefail ## Pipefail, complain on new unassigned variables. + +## Track the version of the TSV_patch template used +VERSION='0.2.0dev' + +## This script is applied to the eager input TSV file locally to edit the dummy +## path to the fastQ files added by `create_eager_input.sh` to a real local +## path provided as a positional argument. Any further local tweaks to the +## TSV before running eager should be added below that in the form of bash +## commands to aid in reproducibility. + +## usage tsv_patch.sh + +local_data_dir="$(readlink -f ${1})" +input_tsv="$(readlink -f ${2})" +output_tsv="$(dirname ${local_data_dir})/$(basename -s ".tsv" ${input_tsv}).finalised.tsv" +columns_to_keep=("Sample_Name" "Library_ID" "Lane" "Colour_Chemistry" "SeqType" "Organism" "Strandedness" "UDG_Treatment" "R1" "R2" "BAM") +source $(dirname ${2})/../../scripts/source_me.sh ## Load helper functions + +## Index non-proliferated columns and exclude them from the finalised TSV +cut_selector='' +tsv_header=($(head -n1 ${input_tsv})) +for col_name in ${columns_to_keep[@]}; do + let idx=$(get_index_of ${col_name} "${columns_to_keep[@]}")+1 ## awk uses 1-based indexing + if [[ ! ${idx} -eq -1 ]]; then + cut_selector+="${idx}," + fi +done + +## Remove added columns, and put columns in right order +cut -f ${cut_selector%,} ${input_tsv} > ${output_tsv} +sed -i -e "s||${local_data_dir}|g" ${output_tsv} + +## Any further commands to edit the file before finalisation should be added below as shown +# sed -ie 's/replace_this/with_this/g' ${output_tsv} + +## Keep track of versions +version_file="$(dirname ${input_tsv})/script_versions.txt" +## Remove versions from older run if there +grep -v -F -e "$(basename ${0})" -e "source_me.sh for final TSV" ${version_file} >${version_file}.new +## Then add new versions +echo -e "$(basename ${0}):\t${VERSION}" >> ${version_file}.new +echo -e "source_me.sh for final TSV:\t${HELPER_FUNCTION_VERSION}" >>${version_file}.new +mv ${version_file}.new ${version_file} diff --git a/packages/2021_Yaka_Anatolia/script_versions.txt b/packages/2021_Yaka_Anatolia/script_versions.txt new file mode 100644 index 0000000..be6857b --- /dev/null +++ b/packages/2021_Yaka_Anatolia/script_versions.txt @@ -0,0 +1,2 @@ +create_eager_input.sh: 0.2.1dev +source_me.sh for initial TSV: 0.2.1dev