CNVkit: Genome-wide copy number from targeted DNA sequencing¶
|License:||Apache License 2.0|
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¶
- File formats
- Tumor heterogeneity
- Whole-genome sequencing and targeted amplicon capture
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: http://dx.doi.org/10.1101/010876
A recent poster presentation is also available on F1000 Posters.