.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH CAT "1" "May 2020" "CAT 5.0.4" "User Commands"
.SH NAME
CAT \- tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
.SH SYNOPSIS
.B CAT
(prepare | contigs | bin | bins | add_names | summarise) [\-v / \fB\-\-version]\fR [\-h / \fB\-\-help]\fR
.SH DESCRIPTION
Run Contig Annotation Tool (CAT) or Bin Annotation Tool (BAT).
.SH OPTIONS
.SS "Required choice:"
.TP
prepare
Download database files and construct databases.
.TP
contigs
Run CAT.
.TP
bin
Run BAT on a single bin.
.TP
bins
Run BAT on a set of bins.
.TP
add_names
Add taxonomic names to CAT or BAT output files.
.TP
summarise
Summarise a named CAT or BAT classification file.
.SS "Optional arguments:"
.TP
\fB\-v\fR, \fB\-\-version\fR
Print version information and exit.
.TP
\fB\-h\fR, \fB\-\-help\fR
Show this help message and exit.
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.