ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads
Autor: | Aleksandar Milosavljevic, Oliver A. Hampton, Christopher A. Miller, Cristian Coarfa |
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Rok vydání: | 2011 |
Předmět: |
Chromosome Structure and Function
Gene Dosage lcsh:Medicine Genomics Computational biology Biology Genome DNA sequencing 03 medical and health sciences 0302 clinical medicine Software Genome Analysis Tools Genetics Cancer Genetics Genome Sequencing lcsh:Science Paired-end tag 030304 developmental biology Comparative genomics 0303 health sciences Models Statistical Multidisciplinary Massive parallel sequencing Base Sequence Chromosome Biology Software Tools business.industry lcsh:R Computational Biology Software Engineering Statistical model 030220 oncology & carcinogenesis Computer Science lcsh:Q Neural Networks Computer business Sequence Analysis Research Article |
Zdroj: | PLoS ONE, Vol 6, Iss 1, p e16327 (2011) PLoS ONE |
ISSN: | 1932-6203 |
Popis: | 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/. |
Databáze: | OpenAIRE |
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