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README.md

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Configurations for the analysis

Parameters to set

To run the analysis four file paths and directories are required as input. The default files are listed in the 'nextflow.config' and can be changed with the following parameters added to the run command:

File Command
Primer --primers "file path"
Adapter --adapters "file path"
InitDir --initDir "file path"
Configurations --config "directory path"

Description of files

Below follows a description of the files that are made available in this directory.

Primers

Version File Primer type Description
1 A_primers_6AMP_PCR1-2.fasta A 6 primer pairs, PCR1+PCR2
2 A_primers_6AMP_PCR1.fasta A 6 primer pairs, PCR1
3 A_primers_6AMP_PCR1_F4-Bprimers.fasta A+B 6 primer pairs, PCR1, B primers used for fragment 4
4 B_primers_1AMP_PCR1-2.fasta B 1 primer pair, PCR1+PCR2
5 AB_primers_1AMP_PCR1.fasta A, B 1 primer pair, PCR1, A and B primers are identical
6 B_primers_6AMP_PCR1-2.fasta B 6 primer pairs, PCR1+PCR2
7 B_primers_6AMP_PCR1.fasta B 6 primer pairs, PCR1

Adapters

Version Adapters Description
1 NexteraPE-PE.fa Nextera paired-end adapters

Shiver configuration file

Version Configurations Description
1 original_config.sh Default settings used in Shiver
2 shiver_config_BQ20_notrimming.sh TIME-study settings

Configuration file 2

The following options in Shiver are altered. For the full list of options see the default config.

Parameter Value Default Description
TrimReadsForAdaptersAndQual false true Trim adapaters and low quality bases from reads using trimmomatic?
TrimReadsForPrimers false true Trim exact matches to PCR primers from the end of reads using fastaq?
mpileupOptions --min-BQ 20 --min-BQ 5 Higher quality threshold for individual bases
deduplicate true false Remove read pairs marked as duplicates? This can cause loss of diversity in the reads due to true biological variation as well sequencing error.

Shiver init directory

Version InitDir Description
1 InitDirShiver220516_BQ20_1AMP_Bprimers_PCR1 1 amplicon primers, 2020 references (no UTRs), primers: B, PCR1
2 InitDirShiver220516_BQ20_1AMP_Bprimers_PCR2 1 amplicon primers, 2020 references (no UTRs), primers: B, PCR1+PCR2
3 InitDirShiver220516_BQ20_6AMP_ABprimers_PCR1 6 amplicon primers, 2020 references (no UTRs), primers: A+B(F4), PCR1
4 InitDirShiver220516_BQ20_6AMP_Aprimers_PCR1-2 6 amplicon primers, 2020 references (no UTRs) primers: A, PCR1+2
5 InitDirShiver220516_BQ20_6AMP_Aprimers_PCR1 6 amplicon primers, 2020 references (no UTRs), primers: A, PCR1
6 InitDirShiver220525_BQ20_6AMP_Bprimers_PCR1 6 amplicon primers, 2020 references (no UTRs), primers: B, PCR1

References to use in Shiver alignments

Reference compendiums with representative genomes can be downloaded from the LANL HIV database.

Reference file Description
HIV1_COM_2020_genome_DNA.fasta Represenative genome alignment with references from 2020 and earlier.
HIV1_COM_2020_547-9592_DNA.fasta Represenative genome alignment with references from 2020 and earlier. Genomic positions 547-9592 included.
HIV1_COM_2017_547-9592_DNA_2018Compendium.fasta Represenative genome alignment with references from 2018 and earlier. Genomic positions 547-9592 included.