PopMAG: A Nextflow pipeline for population genetics analysis based on Metagenome-Assembled Genomes

Abstract Metagenome-assembled genomes (MAGs) are routinely recovered from metagenomic studies, yet the population genetic information embedded within these datasets remains largely underutilized. Analyzing within-species genetic variation can reveal adaptive evolution, selection pressures, and ecological dynamics that are hidden when MAGs are treated as homogeneous entities. Existing tools address individual analysis steps in isolation, requiring manual integration and creating barriers for researchers without extensive bioinformatics expertise. Here we present PopMAG, a Nextflow pipeline and interactive Shiny application that automates population genetics analysis of MAGs. PopMAG integrates quality control, community profiling, competitive read mapping, functional annotation, and microdiversity estimation into a single reproducible workflow. The pipeline calculates key population genetics metrics including nucleotide diversity (π), pN/pS ratios, fixation index (FST), Levins’ index and SNVs counts with results consolidated into an interactive visualization platform for metadata-driven exploration. We demonstrate PopMAG’s utility through analysis of longitudinal cystic fibrosis lung metagenomes, where we detect signatures of antibiotic-driven selection in Pseudomonas aeruginosa efflux pump genes coinciding with treatment intervention. Availability and implementation PopMAG and corresponding documentation are publicly available at https://github.com/daasabogalro/PopMAG. Competing Interest Statement The authors have declared no competing interest.