PopGLen-a Snakemake pipeline for performing population genomic analyses using genotype likelihood-based methods.

Bioinformatics 41 (3) - [2025-03-04; online 2025-03-12]

PopGLen is a Snakemake workflow for performing population genomic analyses within a genotype-likelihood framework, integrating steps for raw sequence processing of both historical and modern DNA, quality control, multiple filtering schemes, and population genomic analysis. Currently, the population genomic analyses included allow for estimating linkage disequilibrium, kinship, genetic diversity, genetic differentiation, population structure, inbreeding, and allele frequencies. Through Snakemake, it is highly scalable, and all steps of the workflow are automated, with results compiled into an HTML report. PopGLen provides an efficient, customizable, and reproducible option for analyzing population genomic datasets across a wide variety of organisms. PopGLen is available under GPLv3 with code, documentation, and a tutorial at https://github.com/zjnolen/PopGLen. An example HTML report using the tutorial dataset is included in the Supplementary Material.

Bioinformatics (NBIS) [Service]

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Bioinformatics Support, Infrastructure and Training [Service]

PubMed 40067089

DOI 10.1093/bioinformatics/btaf105

Crossref 10.1093/bioinformatics/btaf105

pmc: PMC11932725
pii: 8069456