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amr-detection

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Profiles the antimicrobial-resistance gene content (resistome) of shotgun metagenomes - read-based quantification with RGI bwt, AMR++/MEGARes, ARGs-OAP/SARG, deepARG, or GROOT, and presence calling with AMRFinderPlus/ABRicate on assembled contigs or MAGs. Covers why an ARG hit is a sequence match not a phenotype, why a metagenomic ARG has no host and no genomic context until assembly (and assembly breaks at ARGs), per-gene curated thresholds vs a flat 80/80, gene-fraction false-positive control, and cross-study normalization pitfalls. Use when quantifying a community resistome, normalizing ARG abundance, or calling ARGs from metagenome contigs. For pure-culture isolate AMR, point mutations, and phenotype/MIC prediction see epidemiological-genomics/amr-surveillance.

When to use

• quantifying a community resistome
• normalizing ARG abundance
• calling ARGs from metagenome contigs
• read-based quantification with RGI bwt
• presence calling with AMRFinderPlus/ABRicate

When not to use

• pure-culture isolate AMR
• point mutations
• phenotype/MIC prediction
• in-silico antibiogram
• MLST/clone/outbreak context
• GLASS reporting
• assembly/binning and ARG-host linkage mechanics
• general gene-family/pathway abundance

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