# 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.