KLEBORATE

NAME

kleborate - tool to screen Klebsiella genome assemblies

SYNOPSIS

kleborate -a 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]

DESCRIPTION

Kleborate: a tool for characterising virulence and resistance in Klebsiella

OPTIONS

Required arguments:

-a ASSEMBLIES [ASSEMBLIES ...], --assemblies ASSEMBLIES [ASSEMBLIES ...]

FASTA file(s) for assemblies

Screening options:

-r, --resistance

Turn on resistance genes screening (default: no resistance gene screening)

-s, --species

Turn on Klebsiella species identification (requires Mash, default: no species identification)

--kaptive_k

Turn on Kaptive screening of K loci (default: do not run Kaptive for K loci)

--kaptive_o

Turn on Kaptive screening of O loci (default: do not run Kaptive for O loci)

-k, --kaptive

Equivalent to --kaptive_k --kaptive_o

--all

Equivalent to --resistance --species --kaptive

Output options:

-o OUTFILE, --outfile OUTFILE

File for detailed output (default: Kleborate_results.txt)

--kaptive_k_outfile KAPTIVE_K_OUTFILE

File for full Kaptive K locus output (default: do not save Kaptive K locus results to separate file)

--kaptive_o_outfile KAPTIVE_O_OUTFILE

File for full Kaptive O locus output (default: do not save Kaptive O locus results to separate file)

Help:

-h, --help

Show this help message and exit

--version

Show program’s version number 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.