Workflow Type: Galaxy
Open
Frozen
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 |
---|---|---|---|
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 |
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Paired Collection | Paired Collection | Illumina reads with fastqsanger encoding |
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Steps
ID | Name | Description |
---|---|---|
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 |
---|---|---|---|
fastp_pe | fastp_pe | n/a |
|
fastp_html_report | fastp_html_report | n/a |
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Map with BWA-MEM on input dataset(s) (mapped reads in BAM format) | Map with BWA-MEM on input dataset(s) (mapped reads in BAM format) | n/a |
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filtered_mapped_reads | filtered_mapped_reads | n/a |
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mapped_reads_stats | mapped_reads_stats | n/a |
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markduplicates_stats | markduplicates_stats | n/a |
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markduplicates_reads | markduplicates_reads | n/a |
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realigned_deduplicated_filtered_mapped_reads | realigned_deduplicated_filtered_mapped_reads | n/a |
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preprocessing_and_mapping_reports | preprocessing_and_mapping_reports | n/a |
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realigned_deduplicated_filtered_mapped_reads_with_indel_quals | realigned_deduplicated_filtered_mapped_reads_with_indel_quals | n/a |
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called_variants | called_variants | n/a |
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soft_filtered_variants | soft_filtered_variants | n/a |
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annotated_variants | annotated_variants | n/a |
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annotated_variants_stats | annotated_variants_stats | n/a |
|
Version History
v0.2.2 (latest) Created 21st Dec 2021 at 03:01 by WorkflowHub Bot
Updated to v0.2.2
Open
master
7df401a
v0.1 (earliest) Created 12th Mar 2021 at 13:41 by WorkflowHub Bot
Added/updated 8 files
Frozen
master
cff7a1e
Creators and Submitter
Creators
Not specifiedAdditional credit
Wolfgang Maier
Submitter
License
Activity
Views: 7777 Downloads: 1407 Runs: 1
Created: 12th Mar 2021 at 13:41
Last updated: 21st Dec 2021 at 03:01
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