The AMRFinderPlus software and the accompanying database are designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences. We have also added "plus" stress, heat, and biocide resistance and virulence factors for some organisms.
See the AMRFinderPlus wiki for documentation of the software and database.
To build the image use the script build-image.sh which will grab the latest versions of software and database from the internet to facilitate tagging of the resulting image.
docker run --rm -v ${PWD}:/data ncbi/amr \ amrfinder -p test_prot.fa --threads 8 > amrfinder.out Note that this image contains both software and database. It is updated at dockerhub with every software and database release, so if your docker image is up-to-date then you shouldn't need to update the database to get the latest results.
docker run --rm -v ${PWD}:/data ncbi/amr \ bash -c 'amrfinder -u && amrfinder -p test_prot.fa --threads 8' \ > amrfinder.out See Running AMRFinderPlus for details on AMRFinderPlus command-line options.
