sars-cov-2-pe-illumina-wgs-variant-calling/COVID-19-PE-WGS-ILLUMINA
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Download RO CrateCOVID-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 and SubmitterViews: 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
AttributionsNone
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https://orcid.org/0000-0001-8271-5429
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