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.


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[]


ID Name Description
3 fastp
4 SnpEff build:
5 Map with BWA-MEM
6 Samtools view
7 MarkDuplicates
8 Samtools stats
9 Realign reads
10 MultiQC
11 Insert indel qualities
12 Call variants
13 Lofreq filter
14 SnpEff eff:


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

Version History

v0.1 (earliest) Created 4th Jun 2022 at 03:01 by WorkflowHub Bot

Updated to v0.1

Frozen v0.1 10e094e
help Creators and Submitter
Not specified
Additional credit

Anton Nekrutenko


Views: 2006   Downloads: 111

Created: 4th Jun 2022 at 03:01

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Total size: 1.01 MB
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