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nf-core/eager: Citations

nf-core

Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

Nextflow

Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

Pipeline tools

  • FastQC

    Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

  • MultiQC

    Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

  • Falco

    de Sena Brandine, G., Smith, A.D. (2019). Falco: high-speed FastQC emulation for quality control of sequencing data. F1000Res., 8, 1874. doi: 10.12688%2Ff1000research.21142.2

  • fastp

    Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics , 34(17), i884–i890. doi: 10.1093/bioinformatics/bty560

  • AdapterRemoval

    Schubert, M., Lindgreen, S., & Orlando, L. (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 9, 88. doi: 10.1186/s13104-016-1900-2

  • Picard Tools

    Broad Institute (2019). Picard Toolkit. GitHub Repository: https://broadinstitute.github.io/picard/

  • SeqKit

    Shen, W., Le, S., Li, Y., & Hu, F. (2016). SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLOS ONE, 11(10), e0163962. doi:10.1371/journal.pone.0163962

  • bwa

    Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics , 25(14), 1754–1760. doi: 10.1093/bioinformatics/btp324

  • BWA-MEM

    Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv , arXiv:1303.3997. doi: 10.48550/arXiv.1303.3997

  • Bowtie 2

    Langmead, B., Salzberg, S. (2012). Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357–359. doi: 10.1038/nmeth.1923

    Langmead, B., Wilks, C., Antonescu, V., Charles, R. (2018). Scaling read aligners to hundreds of threads on general-purpose processors. Bioinformatics, 35(3), doi: 10.1093/bioinformatics/bty648

  • SAMtools

    Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics , 25(16), 2078–2079. doi: 10.1093/bioinformatics/btp352

  • DeDup

    Peltzer, A., Jäger, G., Herbig, A., Seitz, A., Kniep, C., Krause, J., & Nieselt, K. (2016). EAGER: efficient ancient genome reconstruction. Genome Biology, 17(1), 1–14. doi: 10.1186/s13059-016-0918-z

  • ANGSD

    Korneliussen, T. S., Albrechtsen, A., Nielsen, R. (2014) ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics, 15, 356. doi: 10.1186/s12859-014-0356-4

    Rasmussen, M., et. al. (2011) An Aboriginal Australian genome reveals separate human dispersals into Asia. Science, 334(6052), 94-98. doi: 10.1126/science.1211177

  • prinseqplusplus

    Cantu VA, Sadural J, Edwards R. 2019. PRINSEQ++, a multi-threaded tool for fast and efficient quality control and preprocessing of sequencing datasets. PeerJ Preprints 7:e27553v1. doi: 10.7287/peerj.preprints.27553v1

  • bbduk

    Bushnell B, Rood J, Singer E (2017) BBMerge – Accurate paired shotgun read merging via overlap. PLOS ONE 12(10): e0185056. https://doi.org/10.1371/journal.pone.0185056

  • BEDTools

    Quinlan, A. R., & Hall, I. M. (2010). BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics, 26(6), 841–842. https://doi.org/10.1093/bioinformatics/btq033

  • PreSeq

    Daley, T., & Smith, A. D. (2013). Predicting the molecular complexity of sequencing libraries. Nature Methods, 10(4), 325–327. doi: 10.1038/nmeth.2375

  • endorS.py

    Fellows Yates JA, Lamnidis TC, Borry M, Valtueña Andrades A, Fagernäs Z, Clayton S, Garcia MU, Neukamm J, Peltzer A. 2021. Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ 9:e10947. doi: 10.7717/peerj.10947

  • mapDamage2

    Jónsson H, Ginolhac A, Schubert M, Johnson P, Orlando L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 2013. 23rd April 2013. doi: 10.1093/bioinformatics/btt193

  • PMDtools

    Skoglund P., Northoff B.H.,Shunkov M.V., Derevianko A., Pääbo S., Krause J., Jakobsson M. (2014) Separating ancient DNA from modern contamination in a Siberian Neandertal, Proceedings of the National Academy of Sciences USA doi: 10.1073/pnas.1318934111

  • BamUtils

    Jun, G., Wing, M. K., Abecasis, G. R., & Kang, H. M. (2015). An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data. Genome Research, 25(6), 918–925. doi: 10.1101/gr.176552.114

  • QualiMap

    QualiMap Okonechnikov, K., Conesa, A., & García-Alcalde, F. (2016). Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics , 32(2), 292–294. doi: 10.1093/bioinformatics/btv566.

  • DamageProfiler

    DamageProfiler Neukamm, J., Peltzer, A., & Nieselt, K. (2020). DamageProfiler: Fast damage pattern calculation for ancient DNA. In Bioinformatics (btab190). doi: 10.1093/bioinformatics/btab190.

  • GATK 3.5

    DePristo M, Banks E, Poplin R, Garimella K, Maguire J, Hartl C, Philippakis A, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell T, Kernytsky A, Sivachenko A, Cibulskis K, Gabriel S, Altshuler D, Daly M. (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics, 43(5), 491–498. doi: 10.1038/ng.806.

  • GATK 4.X

    Poplin R, Ruano-Rubio V, DePristo MA, Fennell TJ, Carneiro MO, Van der Auwera GA, Kling DE, Gauthier LD, Levy-Moonshine A, Roazen D, Shakir K, Thibault J, Chandran S, Whelan C, Lek M, Gabriel S, Daly MJ, Neale B, MacArthur DG, Banks E. (2017). Scaling accurate genetic variant discovery to tens of thousands of samples bioRxiv, 201178. doi: 10.1101/201178.

  • FreeBayes

    Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012. doi: 10.48550/arXiv.1207.3907.

  • BCFtools

    Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics (2011) 27(21) 2987-93.doi: 10.1093/bioinformatics/btr509.

    Sex.DetERRmine.py Lamnidis, T.C. et al., 2018. Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe. Nature communications, 9(1), p.5018. Available at: http://dx.doi.org/10.1038/s41467-018-07483-5. Download: https://github.com/TCLamnidis/Sex.DetERRmine

  • MALT

    Vågene, Å.J., Herbig, A., Campana, M.G., Nelly, M., García, R., Warinner, C., Sabin, S., Spyrou, M.A., Valtueña, A.A., Huson, D., Tuross, N., Bos, K.I. & Krause, J. (2018). Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico. Nat Ecol Evol 2, 520–528. doi: 10.1038/s41559-017-0446-6

  • HOPS

    Hübler, R., Key, F.M., Warinner, C. et al. (2019). HOPS: automated detection and authentication of pathogen DNA in archaeological remains. Genome Biol 20, 280. doi: 10.1186/s13059-019-1903-0

  • MEGAN

    Huson DH, Beier S, Flade I, Górska A, El-Hadidi M, Mitra S, et al. (2016) MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PLoS Comput Biol 12(6): e1004957. doi: [10.1371/journal.pcbi.1004957] https://doi.org/10.1371/journal.pcbi.1004957

  • Kraken2

    Wood, Derrick E., Jennifer Lu, and Ben Langmead. 2019. Improved Metagenomic Analysis with Kraken 2. Genome Biology 20 (1): 257. doi: 10.1186/s13059-019-1891-0.

  • KrakenUniq

    Breitwieser, Florian P., Daniel N. Baker, and Steven L. Salzberg. 2018. KrakenUniq: confident and fast metagenomics classification using unique k-mer counts. Genome Biology 19 (1): 198. doi: 10.1186/s13059-018-1568-0

  • MetaPhlAn

    Blanco-Míguez, A., Beghini, F., Cumbo, F. et al. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nat Biotechnol (2023). doi: 10.1038/s41587-023-01688-w

  • TAXPASTA

    Beber et al., (2023). TAXPASTA: TAXonomic Profile Aggregation and STAndardisation. Journal of Open Source Software, 8(87), 5627, doi: 10.21105/joss.05627

  • CircularMapper

    Peltzer, A., Jäger, G., Herbig, A., Seitz, A., Kniep, C., Krause, J., & Nieselt, K. (2016). EAGER: efficient ancient genome reconstruction. Genome Biology, 17(1), 1–14. doi: 10.1186/s13059-016-0918-z

Software packaging/containerisation tools

  • Anaconda

    Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

  • Bioconda

    Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

  • BioContainers

    da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

  • Docker

    Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

  • Singularity

    Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.