This repo contains the analysis pipeline for a mutation accumulation experiment D. magna (2017--). The pipeline is implemented in Snakemake (docs). See pipe/Snakefile for the main script. For a summary of the pipeline implementation see pipe/README.md.
Dependencies:
- https://github.com/fennerm/fmbiopy
- https://github.com/fennerm/fen.R.util
- snakemake
- samtools
- SPAdes
- diamond blastx
- sambamba
- blobtools
- picard
- bowtie2
- BBMap
- blastn
- QUAST
- BUSCO
- fastqc
- multiqc
- bioawk
- GATK