MagSTREAM: a Snakemake pipeline for genome-resolved metagenomics, ARG-MGE co-localization, and antimicrobial resistance surveillance from Oxford Nanopore metagenomic assemblies

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MagSTREAM is a reproducible Snakemake pipeline for reconstructing, quality-filtering, dereplicating, and taxonomically classifying metagenome-assembled genomes (MAGs) from Oxford Nanopore long-read metagenomic assemblies. It provides genome-resolved antimicrobial resistance gene (RGI/CARD) and mobile genetic element (mobileOG-db) annotation, together with contig-level ARG x MGE co-localization analysis. Developed as a companion to MetaSTREAM for wastewater-based antimicrobial resistance surveillance in Conakry, Guinea.