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/
This workflow is part of the reference-guided stacks workflow, https://workflowhub.eu/workflows/347
- demultiplexed reads in fastq format, may be output from the QC workflow. Files are in a collection.
- reference genome in fasta format
- A set of filtered bam files, ready for the next part of the stacks workflow (e.g. gstacks).
- Statistics on the bam files.
|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|