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.