Workflow Type: Galaxy
Open
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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 | |
report_html | report_html | n/a | |
report_json | report_json | n/a | |
output | output | n/a | |
mapping_stats | mapping_stats | n/a | |
metrics_file | metrics_file | n/a | |
outFile | outFile | n/a | |
stats | stats | n/a | |
plots | plots | n/a | |
html_report | html_report | n/a | |
realigned | realigned | 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
v0.1.3 (latest) Created 21st Dec 2021 at 03:01 by WorkflowHub Bot
Updated to v0.1.3
Open
master
ece9c04
v0.1 (earliest) Created 12th Mar 2021 at 13:41 by WorkflowHub Bot
Added/updated 8 files
Frozen
master
6005b83

Creators
Not specifiedAdditional credit
Wolfgang Maier
Submitter
License
Activity
Views: 1207 Downloads: 36
Created: 12th Mar 2021 at 13:41
Last updated: 21st Dec 2021 at 03:01
Last used: 27th Jun 2022 at 16:50

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