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

SUMMARY: 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.

AVAILABILITY AND IMPLEMENTATION: Source code, demo data and detailed documentation are freely available at https://github.com/JCVenterInstitute/CAMRA.