PopMAG: a Nextflow pipeline for population genetics analysis based on metagenome-assembled genomes
Daniel Sabogal-Rodriguez, Alejandro Caro-Quintero, Michael DeGiorgio · 2026
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Description
Daniel Sabogal-Rodriguez, Alejandro Caro-Quintero, and Michael DeGiorgio present in 2026 PopMAG, a software pipeline for population genetics. It mines genomes built out of DNA from the environment. Such genomes are usually treated as single agreed sequences, which hides the strain-level variety inside them. That variety can reveal adaptation, selection pressure, and shifts in ecology.
PopMAG runs quality checks, species profiling, read mapping, gene labeling, and diversity counts in one flow, with an app for exploring results. It outputs key metrics like nucleotide diversity and selection ratios. A test on cystic fibrosis lung samples over time found signs matching antibiotic-driven selection in drug pump genes of a lung pathogen during treatment.
Catalog record
| CREATOR | Daniel Sabogal-Rodriguez, Alejandro Caro-Quintero, Michael DeGiorgio |
|---|---|
| YEAR | 2026 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 22 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |