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KLEBORATE(1) User Commands KLEBORATE(1)

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:

FASTA file(s) for assemblies

Screening options:

Turn on resistance genes screening (default: no resistance gene screening)
Turn on Klebsiella species identification (requires Mash, default: no species identification)
Turn on Kaptive screening of K loci (default: do not run Kaptive for K loci)
Turn on Kaptive screening of O loci (default: do not run Kaptive for O loci)
Equivalent to --kaptive_k --kaptive_o
Equivalent to --resistance --species --kaptive

Output options:

File for detailed output (default: Kleborate_results.txt)
File for full Kaptive K locus output (default: do not save Kaptive K locus results to separate file)
File for full Kaptive O locus output (default: do not save Kaptive O locus results to separate file)

Help:

Show this help message and exit
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.

September 2019 kleborate 0.3.0