recipe plasmidtron

PlasmidTron: assembling the cause of phenotypes from NGS data



GNU General Public License v3 (GPLv3)



package plasmidtron

(downloads) docker_plasmidtron



depends biopython:

depends kmc:


depends matplotlib:

depends pyfastaq:


depends python:


depends spades:




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 plasmidtron

and update with::

   mamba update plasmidtron

To create a new environment, run:

mamba create --name myenvname plasmidtron

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

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