.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
.TH KLEBORATE "1" "September 2019" "kleborate 0.3.0" "User Commands"
.SH NAME
kleborate \- tool to screen Klebsiella genome assemblies
.SH SYNOPSIS
.B kleborate
\fB\-a\fR ASSEMBLIES [ASSEMBLIES ...] [\-r] [\-s] [\-\-kaptive_k]
[\-\-kaptive_o] [\-k] [\-\-all] [\-o OUTFILE]
[\-\-kaptive_k_outfile KAPTIVE_K_OUTFILE]
[\-\-kaptive_o_outfile KAPTIVE_O_OUTFILE] [\-h] [\-\-version]
.SH DESCRIPTION
Kleborate: a tool for characterising virulence and resistance in Klebsiella
.SH OPTIONS
.SS "Required arguments:"
.TP
\fB\-a\fR ASSEMBLIES [ASSEMBLIES ...], \fB\-\-assemblies\fR ASSEMBLIES [ASSEMBLIES ...]
FASTA file(s) for assemblies
.SS "Screening options:"
.TP
\fB\-r\fR, \fB\-\-resistance\fR
Turn on resistance genes screening (default: no
resistance gene screening)
.TP
\fB\-s\fR, \fB\-\-species\fR
Turn on Klebsiella species identification (requires
Mash, default: no species identification)
.TP
\fB\-\-kaptive_k\fR
Turn on Kaptive screening of K loci (default: do not
run Kaptive for K loci)
.TP
\fB\-\-kaptive_o\fR
Turn on Kaptive screening of O loci (default: do not
run Kaptive for O loci)
.TP
\fB\-k\fR, \fB\-\-kaptive\fR
Equivalent to \fB\-\-kaptive_k\fR \fB\-\-kaptive_o\fR
.TP
\fB\-\-all\fR
Equivalent to \fB\-\-resistance\fR \fB\-\-species\fR \fB\-\-kaptive\fR
.SS "Output options:"
.TP
\fB\-o\fR OUTFILE, \fB\-\-outfile\fR OUTFILE
File for detailed output (default:
Kleborate_results.txt)
.TP
\fB\-\-kaptive_k_outfile\fR KAPTIVE_K_OUTFILE
File for full Kaptive K locus output (default: do not
save Kaptive K locus results to separate file)
.TP
\fB\-\-kaptive_o_outfile\fR KAPTIVE_O_OUTFILE
File for full Kaptive O locus output (default: do not
save Kaptive O locus results to separate file)
.SS "Help:"
.TP
\fB\-h\fR, \fB\-\-help\fR
Show this help message and exit
.TP
\fB\-\-version\fR
Show program's version number 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.