recipe cnvkit

Copy number variant detection from high-throughput sequencing




APACHE / Apache-2.0




biotools: cnvkit, doi: 10.1371/journal.pcbi.1004873, usegalaxy-eu: cnvkit_access, usegalaxy-eu: cnvkit_antitarget, usegalaxy-eu: cnvkit_autobin, usegalaxy-eu: cnvkit_batch, usegalaxy-eu: cnvkit_call, usegalaxy-eu: cnvkit_coverage, usegalaxy-eu: cnvkit_diagram, usegalaxy-eu: cnvkit_fix, usegalaxy-eu: cnvkit_heatmap, usegalaxy-eu: cnvkit_reference, usegalaxy-eu: cnvkit_scatter, usegalaxy-eu: cnvkit_segment, usegalaxy-eu: cnvkit_target, usegalaxy-eu: cnvkit_breaks, usegalaxy-eu: cnvkit_genemetrics, usegalaxy-eu: cnvkit_segmetrics, usegalaxy-eu: cnvkit_sex

package cnvkit

(downloads) docker_cnvkit



depends bioconductor-dnacopy:

depends biopython:


depends matplotlib-base:


depends networkx:


depends numpy:


depends pandas:


depends pomegranate:


depends pyfaidx:


depends pysam:


depends python:


depends r-base:


depends r-cghflasso:

depends reportlab:


depends scikit-learn:


depends scipy:




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 cnvkit

and update with::

   mamba update cnvkit

To create a new environment, run:

mamba create --name myenvname cnvkit

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

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