CNVkit: Genome-wide copy number from targeted DNA sequencing

Author:Eric Talevich
Source code:GitHub
License:Apache License 2.0
Packages:PyPI | Docker | Galaxy | DNAnexus
Article:PLOS Computational Biology
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 have published a paper describing CNVkit. If you use this software in a publication, please cite:

Talevich, E., Shain, A.H., Botton, T., & Bastian, B.C. (2014). CNVkit: Genome-wide copy number detection and visualization from targeted sequencing. PLOS Computational Biology 12(4): e1004873

A poster presentation can be viewed at F1000 Research.

Who else is using CNVkit?

Google Scholar lists some of the studies 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 is also available on the commercial platforms DNAnexus, Bina RAVE, and Diploid InHelix.

Finally, CNVkit can export files to several standard formats that can be used with many other software packages, including BioDiscovery Nexus Copy Number and Integrative Genomics Viewer (IGV).

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