---
name: "kleborate"
section: "1"
platform: "linux"
package: "kleborate"
version: "2.4.1-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/kleborate"
---

# kleborate(1)

tool to screen Klebsiella genome assemblies

## 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.