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:

Eric Talevich, A. Hunter Shain, Thomas Botton, Boris C. Bastian (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.

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