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CAT(1) User Commands CAT(1)


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


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


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


Required choice:

Download database files and construct databases.
Run CAT.
Run BAT on a single bin.
Run BAT on a set of bins.
Add taxonomic names to CAT or BAT output files.
Summarise a named CAT or BAT classification file.

Optional arguments:

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


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