Scroll to navigation
| 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:¶
- -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.
