CNVkit: Genome-wide copy number from high-throughput sequencing

Author:Eric Talevich
Source code:GitHub
License:Apache License 2.0
Packages:PyPI | Docker | Galaxy | DNAnexus
Article:PLOS Computational Biology

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput 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.


If you use this software in a publication, please cite our paper describing CNVkit:

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

Also please cite the supporting paper for the segmentation method you use:

PSCBS and DNAcopy (cbs, the default):
HaarSeg (haar):
Ben-Yaacov, E., & Eldar, Y.C. (2008). A fast and flexible method for the segmentation of aCGH data. Bioinformatics 24(16):i139-45.
CGH Fused Lasso (flasso):
Tibshirani, R., & Wang, P. (2008). Spatial smoothing and hot spot detection for CGH data using the fused lasso. Biostatistics 9(1):18–29

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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