Cocos

Web framework for integrating and running antimicrobial resistance (AMR) prediction models on genomic data. Users upload sequencing reads (Illumina or ONT), an assembly or a Bakta annotation; Cocos discovers which registered models can be applied to the sample, runs the assembly, annotation and gene extraction each model needs, and returns resistance predictions with their provenance (PROV-O, RO-Crate) and a trust level. Models are plug-ins described in RDF with the AMRF application profile and validated with SHACL, so new models can be added without changing the code.