table of contents
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.
September 2019 | kleborate 0.3.0 |