sars-cov-2-se-illumina-wgs-variant-calling/COVID-19-SE-WGS-ILLUMINA (v0.1.2)
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Run on usegalaxy.euCOVID-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 |
Creators and Submitter
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
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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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The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data. Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, ...
