NAME

       CAT_pack - taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

DESCRIPTION

       usage:  CAT_pack  (download  | prepare | contigs | bins | reads | add_names | summarise) [-v / --version]
       [-h / --help]

       Run Contig Annotation Tool (CAT), Bin Annotation Tool (BAT), or Read Annotation Tool (RAT).

   Required choice:
       download
              Download and preprocess data from NCBI nr or GTDB.

       prepare
              Construct database files.

       contigs
              Run CAT.

       bins   Run BAT.

       reads  Run RAT.

       add_names
              Add taxonomic names to CAT, BAT, or RAT output files.

       summarise
              Summarise a named CAT or BAT classification file.

   Optional arguments:
       -v, --version
              Print version information and exit.

       -h, --help
              Show this help message and exit.

CAT_pack 6.0.1                                    November 2025                                      CAT_PACK(1)