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

Source code:GitHub
License:Apache License 2.0
Packages:PyPI | Docker | Galaxy | DNAnexus
Article:PLOS Computational Biology
Consulting:Contact DNAnexus Science

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.
pomegranate (HMM segmentation methods):
Schreiber, J. (2018). pomegranate: Fast and Flexible Probabilistic Modeling in Python. Journal of Machine Learning Research 18(164):1−6.

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