recipe nudup

Marks/removes duplicate molecules based on the molecular tagging technology used in NuGEN products.



GNU Lesser General Public License 3.0



package nudup

(downloads) docker_nudup



depends coreutils:

depends grep:

depends python:


depends samtools:


depends sed:



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 nudup

and update with::

   mamba update nudup

To create a new environment, run:

mamba create --name myenvname nudup

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

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