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
GenBank genome	GenBank genome	n/a	File
Paired Collection	Paired Collection	Illumina reads with fastqsanger encoding	File[]

Steps

ID	Name	Description
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	Type
fastp_pe	fastp_pe	n/a	File
fastp_html_report	fastp_html_report	n/a	File
SnpEff4.3 database for	SnpEff4.3 database for	n/a	File
Fasta sequences for	Fasta sequences for	n/a	File
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	File
filtered_mapped_reads	filtered_mapped_reads	n/a	File
mapped_reads_stats	mapped_reads_stats	n/a	File
markduplicates_reads	markduplicates_reads	n/a	File
markduplicates_stats	markduplicates_stats	n/a	File
preprocessing_and_mapping_reports	preprocessing_and_mapping_reports	n/a	File
realigned_deduplicated_filtered_mapped_reads	realigned_deduplicated_filtered_mapped_reads	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
_anonymous_output_1	_anonymous_output_1	n/a	File
SnpEff eff: on input dataset(s) - stats	SnpEff eff: on input dataset(s) - stats	n/a	File