ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads.
ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads.
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DOI：
10.1371/journal.pone.0016327
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发表时间：
2011-01-31
期刊：
影响因子：
3.7
通讯作者：
Milosavljevic A
中科院分区：
文献类型：
--
作者：
Miller CA;Hampton O;Coarfa C;Milosavljevic A
拷贝数改变是许多遗传病的重要因素，包括癌症。我们提出了R的readDepth包，它可以通过测量通过大规模并行测序获得的基因组覆盖深度来检测这些像差。除了获得比现有包更高的精确度外，我们的工具还利用多核架构来并行处理这些大型数据集，从而运行得更快。与其他已发表的方法不同，ReadDepth不需要对参考样本进行排序，并使用了考虑数据过度分散的稳健统计模型。它包括一种通过利用来自配对末端测序的断点信息来进行位置精化来有效提高从低覆盖率实验中获得的分辨率的方法。我们还展示了一种使用全基因组亚硫酸氢盐测序产生的读数来推断拷贝数的方法，从而使表观基因组和拷贝数改变的综合研究成为可能。最后，我们将该工具应用于两个基因组，表明它在低覆盖率和高覆盖率的基因组测序上都表现得很好。ReadDepth包在Linux和MacOSX上运行，是在Apache2.0许可下发布的，可以在http://code.google.com/p/readdepth/.上获得
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/.
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