This repo contains the analysis pipeline for a mutation accumulation project in D. magna and D. pulex (2016-). The pipeline is implemented in Snakemake (docs). See pipe/Snakefile for the main script.
Dependencies:
- https://github.com/fennerm/fmbiopy
- https://github.com/fennerm/fen.R.util
- snakemake
- samtools
- sambamba
- picard
- bowtie2
- BBMap
- fastqc
- multiqc
- GATK
- bamtools
- qualimap