recipe taranis

Pipeline for wg/cgMLST allele calling






Taranis is a allele calling software for cg/wgMLST analysis using bacterial strain assemblies and an available cg/wgMLST schema.

package taranis

(downloads) docker_taranis



depends biopython:


depends blast:


depends mash:


depends numpy:


depends openpyxl:


depends pandas:


depends plotly:


depends prodigal:


depends progressbar:


depends prokka:


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 taranis

and update with::

   mamba update taranis

To create a new environment, run:

mamba create --name myenvname taranis

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 `taranis/tags`_ for valid values for ``<tag>``)

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