recipe targqc

Target capture coverage QC



GPL3 / GNU General Public License v3 (GPLv3)



package targqc

(downloads) docker_targqc



depends beautifulsoup4:

depends bedtools:


depends bwa:

depends click:

depends coverage:

depends gffutils:

depends ipyparallel:

depends ipython:

depends ipython-cluster-helper:

depends joblib:

depends lxml:

depends natsort:

depends nose:

depends numpy:

depends pandas:

depends pip:

depends pybedtools:

depends pysam:

depends python:


depends qualimap:

depends sambamba:


depends six:

depends tempita:



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 targqc

and update with::

   mamba update targqc

To create a new environment, run:

mamba create --name myenvname targqc

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

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