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.