This workflow does not specify a "main" workflow file.
Workflow Type: Galaxy
Generic 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. The reference genome can be provided as a GenBank file.
Inputs
ID | Name | Description | Type |
---|---|---|---|
GenBank genome | GenBank genome | GenBank with annotations for the genome of interest |
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Name for genome database | Name for genome database | Should describe your reference genome, e.g. mpxv for Monkeypox virus. |
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Paired Collection | Paired Collection | Illumina reads with fastqsanger encoding |
|
Steps
ID | Name | Description |
---|---|---|
3 | fastp | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0 |
4 | SnpEff build: | toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4 |
5 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2 |
6 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy1 |
7 | MarkDuplicates | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2 |
8 | Samtools stats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 |
9 | Realign reads | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0 |
10 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0 |
11 | Insert indel qualities | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0 |
12 | Call variants | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1 |
13 | Lofreq filter | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0 |
14 | SnpEff eff: | toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
fastp_pe | fastp_pe | n/a |
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fastp_html_report | fastp_html_report | n/a |
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SnpEff4.3 database | SnpEff4.3 database | n/a |
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Fasta sequences for genbank file | Fasta sequences for genbank file | n/a |
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bwa_mem_alignments | bwa_mem_alignments | n/a |
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filtered_alignment | filtered_alignment | 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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mapped_reads_stats | mapped_reads_stats | 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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SnpEff eff: stats | SnpEff eff: stats | n/a |
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SnpEff variants | SnpEff variants | n/a |
|
Version History
v0.1 (earliest) Created 4th Jun 2022 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
10e094e