ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads.

ABSTRACT: Copy number alterations are important contributors to many genetic diseases, including cancer. We present the readDepth package for R, which can detect these aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. In addition to achieving higher accuracy than existing packages, our tool runs much faster by utilizing multi-core architectures to parallelize the processing of these large data sets. In contrast to other published methods, readDepth does not require the sequencing of a reference sample, and uses a robust statistical model that accounts for overdispersed data. It includes a method for effectively increasing the resolution obtained from low-coverage experiments by utilizing breakpoint information from paired end sequencing to do pos

SUBMITTER: Miller CA 

PROVIDER: S-EPMC3031566 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature