generic-variant-calling-wgs-pe/main
Version 1

View on GitHub

Download RO Crate

Run on usegalaxy.eu

This workflow does not specify a "main" workflow file.

Workflow Type: Galaxy

Tests Passing

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.

SEEK ID: https://workflowhub.eu/workflows/357?version=1

Inputs

ID	Name	Description	Type
GenBank genome	GenBank genome	GenBank with annotations for the genome of interest	File
Name for genome database	Name for genome database	Should describe your reference genome, e.g. mpxv for Monkeypox virus.	string
Paired Collection	Paired Collection	Illumina reads with fastqsanger encoding	File[]

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	File
fastp_html_report	fastp_html_report	n/a	File
SnpEff4.3 database	SnpEff4.3 database	n/a	File
Fasta sequences for genbank file	Fasta sequences for genbank file	n/a	File
bwa_mem_alignments	bwa_mem_alignments	n/a	File
filtered_alignment	filtered_alignment	n/a	File
markduplicates_stats	markduplicates_stats	n/a	File
markduplicates_reads	markduplicates_reads	n/a	File
mapped_reads_stats	mapped_reads_stats	n/a	File
realigned_deduplicated_filtered_mapped_reads	realigned_deduplicated_filtered_mapped_reads	n/a	File
preprocessing_and_mapping_reports	preprocessing_and_mapping_reports	n/a	File
realigned_deduplicated_filtered_mapped_reads_with_indel_quals	realigned_deduplicated_filtered_mapped_reads_with_indel_quals	n/a	File
called_variants	called_variants	n/a	File
soft_filtered_variants	soft_filtered_variants	n/a	File
SnpEff eff: stats	SnpEff eff: stats	n/a	File
SnpEff variants	SnpEff variants	n/a	File