Scroll to navigation

CAT(1) User Commands CAT(1)

NAME

CAT - tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

SYNOPSIS

CAT (prepare | contigs | bin | bins | add_names | summarise) [-v / --version] [-h / --help]

DESCRIPTION

Run Contig Annotation Tool (CAT) or Bin Annotation Tool (BAT).

OPTIONS

Required choice:

prepare
Download database files and construct databases.
contigs
Run CAT.
bin
Run BAT on a single bin.
bins
Run BAT on a set of bins.
add_names
Add taxonomic names to CAT or BAT 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.

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
May 2020 CAT 5.0.4