Abby Williams, University of Oxford, 2025
A pipeline for mapping raw Illumina sequencing reads from avian museum samples to the Zosterops lateralis pseudochromosome assembly.
Workflow
Specific steps are outlined below:
- Index the genome using BWA-MEM2
- Map reads to the Zosterops lateralis pseudochrome assembly using BWA-MEM2
- Deduplication using PicardMarkDuplicates
- Calculate mapping stats and depth using Samtools
- Assess DNA damage using MapDamage2
Installation and usage
Use conda/mamba to install the environment from the environment.yaml provided.
conda create --prefix ./snakemake-env --file environment.yaml
Do the following prior to running:
- edit file paths in
config/config.yaml - add any appropriate profiles in
profiles/ - edit the
run.shdepending on your HPC environment
To run snakemake, run:
sbatch run.sh
This pipeline was built in snakemake using this workflow template.