BALROG-ISO: a high-throughput pipeline for Bacterial AntimicrobiaL Resistance annOtation of Genomes-ISOlate whole genome

BALROG-ISO is a Nextflow pipeline for automated analysis of whole genome sequences of bacterial isolates to perform taxonomic classification, genomic annotation, annotation of antimicrobial resistance genes (ARGs), and prediction of ARG origin (e.g., plasmid, chromosomal). A final summary report additionally offers a comprehensive and user-friendly visualization of key quality metrics and annotation results. BALROG-ISO minimizes command inputs and streamlines modular processes, enabling the concurrent analysis of more genomic samples while also reducing manual job submission and analysis inconsistencies. Overall, BALROG-ISO is an adaptable workflow pipeline optimized for a One Health approach to the exploration of antimicrobial resistance in bacterial genomes.