cAMRah: a scalable and portable workflow for harmonized antimicrobial resistance gene prediction from bacterial genomes

Matute DL, Clarke TH, LaPointe AR, Singh I, Fouts DE

PMID: 41710351

Abstract

cAMRah is a curated workflow designed to predict antimicrobial resistance (AMR) genes in microbial genomes, either in the cloud or on any personal computer running Docker containers. Numerous AMR gene-finding packages exist, each utilizing different algorithms and prediction methods. cAMRah adopts a consensus-based approach to AMR prediction, recognizing that no single tool can identify all AMR genes. It integrates and runs six AMR-finder tools and databases (with plans for future expansion), scores the AMR predictions, maps all results to CDS coordinates and harmonizes the annotation, resulting in consistent gene symbols and ontologies.