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.

kleborate 0.3.0                                  September 2019                                     KLEBORATE(1)