Partial ref-guided workflow - bwa mem only
Version 1

Workflow Type: Galaxy

workflow-partial-bwa-mem

These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using the tools from the Stacks program.

Galaxy Australia: https://usegalaxy.org.au/

Stacks: http://catchenlab.life.illinois.edu/stacks/

This workflow is part of the reference-guided stacks workflow, https://workflowhub.eu/workflows/347

Inputs

  • demultiplexed reads in fastq format, may be output from the QC workflow. Files are in a collection.
  • reference genome in fasta format

Outputs

  • A set of filtered bam files, ready for the next part of the stacks workflow (e.g. gstacks).
  • Statistics on the bam files.

Steps

ID Name Description
2 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0
3 Samtools view: filters out unmapped and non-primary mapped reads (see flags) toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2
4 Samtools stats: BAM stats before filtering toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.3
5 Samtools stats: BAM stats after filtering toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.3
6 MultiQC: BAM stats before filtering toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0
7 MultiQC: BAM stats after filtering toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0

Version History

v1.0 (earliest) Created 31st May 2022 at 09:05 by Anna Syme

Update README.md


Frozen v1.0 0883fff
help Creators and Submitter
Creator
Submitter
Activity

Views: 2644

Created: 31st May 2022 at 09:05

Annotated Properties
Topic annotations
Operation annotations
help Tags

This item has not yet been tagged.

help Attributions

None

Total size: 31.5 KB
Powered by
(v.1.14.1)
Copyright © 2008 - 2023 The University of Manchester and HITS gGmbH