AMR Profiling

MAGGIC profiles antimicrobial resistance genes using AMRFinderPlus, running on refined MAGs after binning and quality assessment.

Output Columns

Column	Description
AMR_Gene_Count	Number of hits with Type == "AMR" or Type == "STRESS" (excludes DISINFECTANT and HEAVY_METAL)
AMR_Classes	Semicolon-separated unique AMR classes (e.g., Beta-Lactam;Aminoglycoside)
AMR_Genes	Semicolon-separated unique gene symbols (e.g., blaTEM-1;aadA)

Database

AMRFinderPlus requires a local reference database. Set the path via --amrfinderplus_db or in workflows/conf/maggic.config (or maggic_lr.config):

amrfinderplus_db = /path/to/maggic_dbs/amrfinderplus/latest

See Database-Requirements for download instructions.

MultiQC Integration

The AMR summary appears in the MultiQC Data Summary cards and the Chromosome/Plasmid result tables. Total AMR gene counts and unique classes are aggregated across all bins.