COVID-19-PE-ARTIC-ILLUMINA (v0.1)
Version 1

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 excludes reads derived from such "tainted" amplicons when calculating allele-frequencies of other variants.

Inputs

ID Name Description Type
ARTIC primers to amplicon assignments ARTIC primers to amplicon assignments Six column BED dataset used by ivar trim and ivar removereads for assigning primers to amplicons. Can be retrieved from https://usegalaxy.eu/u/wolfgang-maier/h/covid-19-resources 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
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
Paired Collection Paired Collection Illumina reads from ARTIC assay with fastqsanger encoding 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 ARTIC primers to amplicon assignments Six column BED dataset used by ivar trim and ivar removereads for assigning primers to amplicons. Can be retrieved from https://usegalaxy.eu/u/wolfgang-maier/h/covid-19-resources
1 ARTIC primer BED BED file containing ARTIC primer positions. Can be retrieved from https://usegalaxy.eu/u/wolfgang-maier/h/covid-19-resources
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
3 Paired Collection Illumina reads from ARTIC assay with fastqsanger encoding
4 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
5 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
6 Samtools view toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2
7 ivar trim toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1
8 Samtools stats toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
9 Realign reads toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
10 Insert indel qualities toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0
11 QualiMap BamQC toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3
12 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0
13 Flatten Collection __FLATTEN__
14 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
15 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1
16 ivar removereads toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1
17 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0
18 VCF-VCFintersect: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0
19 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
20 VCF-VCFintersect: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0
21 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
22 SnpEff eff covid19 version toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19

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_bam output_bam n/a
output output n/a
realigned realigned n/a
output output n/a
raw_data raw_data n/a
output_html output_html n/a
variants variants n/a
output output n/a
outvcf outvcf n/a
stats stats n/a
plots plots n/a
html_report html_report n/a
output_bam output_bam n/a
variants variants n/a
out_file1 out_file1 n/a
outfile outfile n/a
out_file1 out_file1 n/a
outvcf outvcf n/a
snpeff_output snpeff_output n/a
statsFile statsFile n/a
Total size: 108 KB
help Creators and Submitter
Creator
  • Wolfgang Maier
Submitter
License
Activity

Views: 283   Downloads: 3

Created: 1st Mar 2021 at 12:11

Last used: 22nd Sep 2021 at 14:37

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Version 1 (earliest) Created 1st Mar 2021 at 12:11 by WorkflowHub Sandbox Bot

Added/updated 7 files


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