sars-cov-2-pe-illumina-artic-variant-calling/COVID-19-PE-ARTIC-ILLUMINA

Workflow Type: Galaxy

COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ARTIC data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming ARTIC primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by ARTIC primer-binding site mutations and, if possible, excludes reads derived from such "tainted" amplicons when calculating allele-frequencies of other variants.

Inputs

ID Name Description Type
Paired Collection Paired Collection Illumina reads from ARTIC assay with fastqsanger encoding n/a
NC_045512.2 FASTA sequence of SARS-CoV-2 NC_045512.2 FASTA sequence of SARS-CoV-2 Fasta sequence for Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome n/a
ARTIC primer BED ARTIC primer BED BED file containing ARTIC primer positions. Can be retrieved from https://usegalaxy.eu/u/wolfgang-maier/h/covid-19-resources n/a
ARTIC primers to amplicon assignments ARTIC primers to amplicon assignments Used by ivar trim and ivar removereads for assigning primers to amplicons. Should have one line of tab-separated primer names per amplicon. Can be retrieved from https://usegalaxy.eu/u/wolfgang-maier/h/covid-19-resources n/a
Read removal maximum AF Read removal maximum AF Maximum allele-frequency allowed for a primer binding site mutation to trigger amplicon removal. Variants with AF values above this threshold are treated as fixed variants, which won't generate amplicon bias. n/a
Read removal minimum AF Read removal minimum AF Minimum allele-frequency required for a candidate primer binding site mutation to trigger amplicon removal. Variants with AF values below this threshold are treated as possible false-positives, which are not worth the coverage loss associated with amplicon removal. n/a
Minimum DP for amplicon bias correction Minimum DP for amplicon bias correction At any given variant site use the amplicon bias-corrected recall only if the depth of coverage of the site retains at least this value after amplicon removal. n/a
intervals intervals runtime parameter for tool SnpEff eff: n/a
transcripts transcripts runtime parameter for tool SnpEff eff: n/a

Steps

ID Name Description
0 Paired Collection Illumina reads from ARTIC assay with fastqsanger encoding
1 NC_045512.2 FASTA sequence of SARS-CoV-2 Fasta sequence for Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome
2 ARTIC primer BED BED file containing ARTIC primer positions. Can be retrieved from https://usegalaxy.eu/u/wolfgang-maier/h/covid-19-resources
3 ARTIC primers to amplicon assignments Used by ivar trim and ivar removereads for assigning primers to amplicons. Should have one line of tab-separated primer names per amplicon. Can be retrieved from https://usegalaxy.eu/u/wolfgang-maier/h/covid-19-resources
4 Read removal maximum AF Maximum allele-frequency allowed for a primer binding site mutation to trigger amplicon removal. Variants with AF values above this threshold are treated as fixed variants, which won't generate amplicon bias.
5 Read removal minimum AF Minimum allele-frequency required for a candidate primer binding site mutation to trigger amplicon removal. Variants with AF values below this threshold are treated as possible false-positives, which are not worth the coverage loss associated with amplicon removal.
6 Minimum DP for amplicon bias correction At any given variant site use the amplicon bias-corrected recall only if the depth of coverage of the site retains at least this value after amplicon removal.
7 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
8 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
9 Samtools view toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2
10 Samtools stats toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
11 Realign reads toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
12 Insert indel qualities toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0
13 ivar trim toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.1+galaxy0
14 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0
15 QualiMap BamQC toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3
16 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
17 Flatten Collection __FLATTEN__
18 ivar removereads toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.3.1+galaxy0
19 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1
20 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0
21 VCF-VCFintersect: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0
22 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
23 VCF-VCFintersect: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0
24 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
25 SnpEff eff covid19 version toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19
26 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0

Outputs

ID Name Description Type
output_paired_coll output_paired_coll n/a
report_html report_html n/a
report_json report_json n/a
bam_output bam_output n/a
outputsam outputsam n/a
output output n/a
realigned realigned n/a
output output n/a
output_bam output_bam n/a
variants variants n/a
raw_data raw_data n/a
output_html output_html n/a
outvcf outvcf n/a
output output n/a
output_bam output_bam n/a
stats stats n/a
plots plots n/a
html_report html_report n/a
variants variants n/a
out_file1 out_file1 n/a
outfile outfile n/a
out_file1 out_file1 n/a
outfile outfile n/a
snpeff_output snpeff_output n/a
statsFile statsFile n/a
outvcf outvcf n/a
help Creators and Submitter
Creator
  • Wolfgang Maier
Submitter
License
Activity

Views: 66   Downloads: 0

Created: 30th Aug 2021 at 17:00

Last updated: 30th Aug 2021 at 17:00

Last used: 22nd Sep 2021 at 12:46

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Version 2 (latest) Created 30th Aug 2021 at 17:00 by Simone Leo

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Version 2 (earliest) Created 30th Aug 2021 at 17:00 by Simone Leo

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