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CAT_PACK(1) User Commands CAT_PACK(1)

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 and preprocess data from NCBI nr or GTDB.
Construct database files.
Run CAT.
Run BAT.
Run RAT.
Add taxonomic names to CAT, BAT, or RAT output files.
Summarise a named CAT or BAT classification file.

Optional arguments:

Print version information and exit.
Show this help message and exit.

November 2025 CAT_pack 6.0.1