Generic variation analysis on WGS PE data
Version 1

Workflow Type: Galaxy

Stable

Generic variant calling

A generic workflow for identification of variants in a haploid genome such as genomes of bacteria or viruses. It can be readily used on MonkeyPox. The workflow accepts two inputs:

A genbank file with the reference genomes
A collection of paired fastqsanger files

The workflow outputs a collection of VCF files for each sample (each fastq pair). These VCF files serve as input to the Reporting workflow.

Workflow can be accessed directly on usegalaxy.org

The general idea of the workflow is:

SEEK ID: https://workflowhub.eu/workflows/353?version=1

Inputs

ID	Name	Description	Type
Paired Collection	Paired Collection	Illumina reads with fastqsanger encoding	n/a
GenBank genome	GenBank genome	n/a	n/a
reads	reads	runtime parameter for tool Call variants	n/a
reference_source	reference_source	runtime parameter for tool Call variants	n/a
invcf	invcf	runtime parameter for tool Lofreq filter	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	Paired Collection	Illumina reads with fastqsanger encoding
1	GenBank genome
2	fastp	toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
3	SnpEff build:	toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4
4	Map with BWA-MEM	toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
5	Samtools view	toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2
6	Samtools stats	toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
7	MarkDuplicates	toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2
8	MultiQC	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1
9	Realign reads	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
10	Insert indel qualities	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0
11	Call variants	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0
12	Lofreq filter	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
13	SnpEff eff:	toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1

Outputs

ID	Name	Description
output_paired_coll	output_paired_coll	n/a
report_html	report_html	n/a
report_json	report_json	n/a
snpeff_output	snpeff_output	n/a
output_fasta	output_fasta	n/a
bam_output	bam_output	n/a
outputsam	outputsam	n/a
output	output	n/a
metrics_file	metrics_file	n/a
outFile	outFile	n/a
stats	stats	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