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 |
Version History
Version 2 (latest) Created 30th Aug 2021 at 17:01 by Simone Leo
No revision comments
Version 1 (earliest) Created 30th Aug 2021 at 17:00 by Simone Leo
No revision comments

Creators
Not specifiedAdditional credit
Wolfgang Maier
Submitter
License
Activity
Views: 516 Downloads: 9
Created: 30th Aug 2021 at 17:00
Last updated: 30th Aug 2021 at 17:01
Last used: 15th Aug 2022 at 13:55

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