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

TitleReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads.
Publication TypeJournal Article
Year of Publication2011
AuthorsMiller, CA, Hampton, O, Coarfa, C, Milosavljevic, A
JournalPLoS One
Volume6
Issue1
Paginatione16327
Date Published2011 Jan 31
ISSN1932-6203
KeywordsBase Sequence, Computational Biology, Gene Dosage, Genome, Models, Statistical, Neural Networks (Computer), Software
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 positional refinement. We also demonstrate a method for inferring copy number using reads generated by whole-genome bisulfite sequencing, thus enabling integrative study of epigenomic and copy number alterations. Finally, we apply this tool to two genomes, showing that it performs well on genomes sequenced to both low and high coverage. The readDepth package runs on Linux and MacOSX, is released under the Apache 2.0 license, and is available at http://code.google.com/p/readdepth/.

DOI10.1371/journal.pone.0016327
Alternate JournalPLoS ONE
PubMed ID21305028
PubMed Central IDPMC3031566
Grant ListR01 HG004009 / HG / NHGRI NIH HHS / United States
R33 CA114151 / CA / NCI NIH HHS / United States
R01-HG004009 / HG / NHGRI NIH HHS / United States
U01 DA025956 / DA / NIDA NIH HHS / United States
R33-CA114151 / CA / NCI NIH HHS / United States
R21 HG004554 / HG / NHGRI NIH HHS / United States
R21-HG004554 / HG / NHGRI NIH HHS / United States