sars-cov-2-pe-illumina-wgs-variant-calling/COVID-19-PE-WGS-ILLUMINA

Workflow Type: Galaxy

COVID-19: variation analysis on WGS PE data

This workflows performs paired end read mapping with bwa-mem 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
Paired Collection Paired 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 Paired 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 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
4 Samtools view toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2
5 Samtools stats toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
6 MarkDuplicates toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2
7 Realign reads toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
8 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1
9 Insert indel qualities toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0
10 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0
11 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
12 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 output n/a
metrics_file metrics_file n/a
outFile outFile n/a
realigned realigned n/a
stats stats n/a
html_report html_report n/a
output output n/a
variants variants n/a
outvcf outvcf n/a
snpeff_output snpeff_output n/a
statsFile statsFile n/a
help Creators and Submitter
Creator
  • Wolfgang Maier
Submitter
License
Activity

Views: 73   Downloads: 0

Created: 30th Aug 2021 at 17:00

Last updated: 30th Aug 2021 at 17:01

Last used: 22nd Sep 2021 at 07:19

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Version History

Version 2 (latest) Created 30th Aug 2021 at 17:01 by Simone Leo

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

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