recipe kleborate

Screening Klebsiella genome assemblies for MLST, sub-species, and other Klebsiella related genes of interest



GPL3 / GNU General Public License v3 or later (GPLv3+)



package kleborate

(downloads) docker_kleborate



depends biopython:


depends blast:


depends kaptive:

depends mash:

depends python:




You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install kleborate

and update with::

   mamba update kleborate

To create a new environment, run:

mamba create --name myenvname kleborate

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `kleborate/tags`_ for valid values for ``<tag>``)

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