Workflow Type: Galaxy

COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ampliconic 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 amplicon primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by 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 required after amplicon bias correction Minimum DP required after 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
Minimum DP_ALT required after amplicon bias correction Minimum DP_ALT required after amplicon bias correction At any given variant site use the amplicon bias-corrected recall only if the depth of variant-supporting reads at the site retains at least this value after amplicon removal. n/a
input input runtime parameter for tool SnpSift Filter n/a
input input runtime parameter for tool Filter failed datasets 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 required after 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 Minimum DP_ALT required after amplicon bias correction At any given variant site use the amplicon bias-corrected recall only if the depth of variant-supporting reads at the site retains at least this value after amplicon removal.
8 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
9 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0
10 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2
11 Samtools view toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2
12 Samtools stats toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
13 Realign reads toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
14 Insert indel qualities toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0
15 ivar trim toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.1+galaxy2
16 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1
17 QualiMap BamQC toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3
18 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
19 SnpSift Filter toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
20 SnpSift Filter toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
21 Filter failed datasets __FILTER_FAILED_DATASETS__
22 Flatten Collection __FLATTEN__
23 ivar removereads toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.3.1+galaxy2
24 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0
25 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1
26 bcftools annotate toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10
27 SnpSift Filter toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
28 VCF-VCFintersect: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0
29 bcftools annotate toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10
30 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
31 SnpEff eff covid19 version toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19
32 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0

Outputs

ID Name Description Type
out1 out1 n/a
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
out1 out1 n/a
output output n/a
output output n/a
output output 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
output_file output_file n/a
output output n/a
out_file1 out_file1 n/a
output_file output_file n/a
outfile outfile n/a
snpeff_output snpeff_output n/a
statsFile statsFile n/a
outvcf outvcf n/a

Version History

v0.5 (latest) Created 12th Feb 2022 at 03:00 by WorkflowHub Bot

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v0.4.2 Created 21st Dec 2021 at 03:01 by WorkflowHub Bot

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v0.1 (earliest) Created 12th Mar 2021 at 13:41 by WorkflowHub Bot

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help Creators and Submitter
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Submitter
Citation
Maier, W. (2022). sars-cov-2-pe-illumina-artic-variant-calling/COVID-19-PE-ARTIC-ILLUMINA. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.110.7
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Views: 6078

Created: 12th Mar 2021 at 13:41

Last updated: 20th Sep 2022 at 10:41

Last used: 7th Dec 2022 at 02:54

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