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

<h4>Summary</h4>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.<h4>Availability and implementation</h4>Source code, demo data and detailed documentation are freely available at https://github.com/JCVenterInstitute/CAMRA.