CNVkit: Genome-wide copy number from targeted DNA sequencing¶
|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.
Command line usage¶
- Copy number calling pipeline
- Plots and graphics
- Text and tabular reports
- Compatibility and other I/O
- Additional scripts
FAQ & How To¶
- Calling copy number gains and losses
- Tumor analysis
- Tumor heterogeneity
- Germline analysis
- Whole-genome sequencing and targeted amplicon capture
- Bias corrections
- File formats
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:
- McCreery, M.Q. et al. (2015). Evolution of metastasis revealed by mutational landscapes of chemically induced skin cancers. Nature Medicine 21, 1514–1520
- Shain, A.H. et al. (2015). Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway. Nature Genetics, 47(10), 1194-1199
- Shain, A.H. et al. (2015). The Genetic Evolution of Melanoma from Precursor Lesions. New England Journal of Medicine, 373(20), 1926-1936
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).