| Author: | Eric Talevich |
|---|---|
| Contact: | eric.talevich@ucsf.edu |
| License: | Apache License 2.0 |
| Source code: | GitHub |
| Packages: | PyPI | Docker | Galaxy | DNAnexus |
| 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.
.. toctree::
quickstart
.. toctree::
:maxdepth: 2
pipeline
plots
reports
importexport
scripts
.. toctree::
:maxdepth: 3
fileformats
bias
calling
heterogeneity
nonhybrid
.. toctree::
:maxdepth: 2
cnvlib
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:
Talevich, E., Shain, A.H., Botton, T., & Bastian, B.C. (2014). CNVkit: Copy number detection and visualization for targeted sequencing using off-target reads. bioRxiv doi: http://dx.doi.org/10.1101/010876
A poster presentation can be viewed at F1000 Research.
Google Scholar lists some of the references 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
- 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 can also :ref:`export` files to several standard formats that can be used with many other software packages.