A snakemake pipeline for the Norfolk Island Zosterops project

Abby Williams, University of Oxford, 2025

A pipeline for mapping raw Illumina sequencing reads from avian museum samples to the Zosterops lateralis pseudochromosome assembly.

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Workflow

Specific steps are outlined below:

1. Index the genome using BWA-MEM2
2. Map reads to the Zosterops lateralis pseudochrome assembly using BWA-MEM2
3. Deduplication using PicardMarkDuplicates
4. Calculate mapping stats and depth using Samtools
5. Assess DNA damage using MapDamage2

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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.sh depending on your HPC environment

To run snakemake, run:

sbatch run.sh

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This pipeline was built in snakemake using this workflow template.