amrfinder_index

amrfinder_index will rebuild the BLAST and HMMER databases in a database directory. This functionality is normally provided by amrfinder -u and amrfinder_update, but is included as a separate program to help with certain unusual scenarios.

Usage:

amrfinder_index [--quiet] [--debug] <database_directory>

Options:

There is a required positional parameter which is the database directory. Note this should be the actual directory containing the database files, not the parent "data" directory (e.g., data/2023-02-23.1).

--quiet or -q Suppress status messages to STDERR

--debug prints the hmmpress and makeblastdb commands to STDOUT prior to running them

Output:

This will generate the AMR.LIB.h3*, AMRProt.p??, and AMR_DNA-*.n?? files in the database directory that are used by HMMER and BLAST when running AMRFinderPlus.