sars-cov-2-se-illumina-wgs-variant-calling/COVID-19-SE-WGS-ILLUMINA (v0.1.2)

Workflow Type: Galaxy

COVID-19: variation analysis on WGS SE data

This workflows performs single end read mapping with bowtie2 followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.

Inputs

ID Name Description Type
Single End Collection Single End Collection Illumina reads 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
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 Single End Collection Illumina reads 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 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
3 Bowtie2 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2
4 MarkDuplicates toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2
5 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1
6 Realign reads toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
7 Insert indel qualities toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0
8 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0
9 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
10 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
out1 out1 n/a input
report_html report_html n/a html
report_json report_json n/a json
output output n/a bam
mapping_stats mapping_stats n/a txt
metrics_file metrics_file n/a txt
outFile outFile n/a bam
stats stats n/a input
plots plots n/a input
html_report html_report n/a html
realigned realigned n/a bam
output output n/a bam
variants variants n/a vcf
outvcf outvcf n/a vcf
snpeff_output snpeff_output n/a vcf
statsFile statsFile n/a html
help Creators and Submitter
Creator
  • Wolfgang Maier
Submitter
License
Activity

Views: 242   Downloads: 19

Created: 12th Mar 2021 at 13:41

Last updated: 27th Jul 2021 at 03:01

Last used: 30th Jul 2021 at 08:14

help Attributions

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Version History

Version 2 (latest) Created 27th Jul 2021 at 03:01 by WorkflowHub Bot

Updated to v0.1.2

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

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