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  • We present a method for copy number detection, implemented in the software package CNVkit, that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy number evenly across the genome. CNVkit is freely available from https://github.com/etal/cnvkit. We implemented CNVkit as a Python 2.7 software package comprising a command-line program, cnvkit.py, and reusable library, cnvlib. CNVkit generates several kinds of plots using the software libraries Biopython [35], Reportlab (http://www.reportlab.com/opensource/) and matplotlib (http://matplotlib.org): CNVkit source code is freely available from https://github.com/etal/cnvkit under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0).
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