The CopyCat R package can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. It achieves higher accuracy than many other packages, and runs quickly by utilizing multi-core architectures to parallelize the processing of these large data sets. Other features include a method for effectively increasing the resolution obtained from low-coverage experiments by utilizing breakpoint information from paired end sequencing to do positional refinement. It can also be used to infer copy number using reads obtained from bisulfite sequencing experiments.
CopyCat is currently under active development, but the beta version is available for use.