Bioinformatics pipeline for analyzing fluctuating selection in the Common Bluetail Damselfly (Ischnura elegans). This project uses low-coverage whole-genome sequencing (lcWGS) to investigate how selection operates across life stages (aquatic nymphs vs. terrestrial adults) and across generations to maintain genetic diversity in natural populations.
This analyses uses PopGLen v0.4.3 as its main tool and its documentation can be found here: https://zjnolen.github.io/PopGLen/v0.4.3/.
Create mamba environment (-n names the environment, -c channels to use, -y auto selects yes to all prompts)
mamba create -n popglen -c conda-forge -c bioconda snakemake snakedeploy singularity snakemake-executor-plugin-slurm -yThe configuratons in profiles/ and config specify paths, resources, and which snakemake rules are to be run.
Each unique user has to make their own profiles/<username>/config.yaml and specify it while running snakemake to avoid permission conflicts.
Each unique analysis would ideally require their own unique config/config.yml to avoid continously changing the dataset yaml option. The config tells snakemake which rules to run using which data (samples.tsv and units.tsv).
# Copy the template and customize them to your system
cp -r profiles/dardel-template profiles/dardel-<username>
cp -r config/config-template.yaml config/config-<dataset>.yaml# Load the module
module load tmux/3.4
# Start a new session with a name
tmux new -s snakemake
# Make sure you are in the FluctSel-Ischnura directory
cd /path/FluctSel-Ischnura
# Activate popglen
mamba activate popglen
# Run this command with YOUR profile and config. Example is using mine.
snakemake --profile profiles/dardel-<username> --configfile config/config-<dataset>.yamlYou can now detach from screen and have snakemake run in the background even if you close your connection/terminal.
- Detach from screen: Press
Ctrl+B, then pressD - Check if it's still running:
tmux ls - Reattach to check progress:
tmux attach -t snakemake - Kill the session:
kill-session -t snakemake
Nolen ZJ, PopGLen—a Snakemake pipeline for performing population genomic analyses using genotype likelihood-based methods, Bioinformatics, Volume 41, Issue 3, March 2025, btaf105, https://doi.org/10.1093/bioinformatics/btaf105
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