CNVkit: Genome-wide copy number from targeted DNA sequencing

Author:Eric Talevich
License:Apache License 2.0
Source code:GitHub
Packages:PyPI | Docker | Galaxy | DNAnexus
Q&A:Biostars | SeqAnswers

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from targeted DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.


We are in the process of publishing a manuscript describing CNVkit. If you use this software in a publication, for now, please cite our preprint manuscript by DOI, like so:

Talevich, E., Shain, A.H., Botton, T., & Bastian, B.C. (2014). CNVkit: Copy number detection and visualization for targeted sequencing using off-target reads. bioRxiv doi:

A poster presentation can be viewed at F1000 Research.

Who is using CNVkit?

Google Scholar lists some of the references where CNVkit has been used by other researchers.

We’d like to highlight:

Specific support for CNVkit is included in bcbio-nextgen, THetA2, and MetaSV; CNVkit can also export files to several standard formats that can be used with many other software packages.

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