kleborate1

Tool to screen klebsiella genome assemblies

Usage

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]

Overview

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