recipe minys

MinYS allows targeted assembly of bacterial genomes using a reference-guided pipeline.






package minys

(downloads) docker_minys



depends bwa:

depends libgcc-ng:


depends libstdcxx-ng:


depends mindthegap:

depends minia:

depends numpy:

depends pyani:

depends python:


depends samtools:



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 minys

and update with::

   mamba update minys

To create a new environment, run:

mamba create --name myenvname minys

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

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