Improving read mapping using additional prefix grams.
Improving read mapping using additional prefix grams.
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DOI：
10.1186/1471-2105-15-42
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发表时间：
2014-02-05
影响因子：
3
通讯作者：
Xie X
中科院分区：
文献类型：
--
作者：
Kim J;Li C;Xie X
下一代测序（NGS）能够以相对较低的成本快速生产数十亿个碱基。将来自下一代测序仪的读数映射到给定的参考基因组是许多测序应用中重要的第一步。流行的读段映射器，如Bowtie和BWA，被优化以返回每个读段的前一个或几个候选位置。然而，识别每个读段的所有映射位置，而不是仅仅一个或几个，在一些测序应用中也很重要，例如用于发现重复区域中的结合位点的ChIP-seq和用于转录物丰度估计的RNA-seq。在这里，我们介绍了Hobbes 2，一个软件包，旨在快速，准确地比对NGS读段，并专门用于识别每个读段的所有映射位置。Hobbes 2使用一种新的技术有效地识别读段的所有映射位置，该技术利用额外的前缀q-gram来改善过滤。我们广泛比较霍布斯2与国家的最先进的读取映射，并表明霍布斯2可以是一个数量级的速度比其他读取映射，同时消耗更少的内存空间，并实现类似的精度。我们提出Hobbes 2来提高读段映射的准确性，专门用于识别每个读段的所有映射位置。Hobbes 2是用C++实现的，源代码可以在http://hobbes.ics.uci.edu上免费下载。
Next-generation sequencing (NGS) enables rapid production of billions of bases at a relatively low cost. Mapping reads from next-generation sequencers to a given reference genome is an important first step in many sequencing applications. Popular read mappers, such as Bowtie and BWA, are optimized to return top one or a few candidate locations of each read. However, identifying all mapping locations of each read, instead of just one or a few, is also important in some sequencing applications such as ChIP-seq for discovering binding sites in repeat regions, and RNA-seq for transcript abundance estimation. Here we present Hobbes2, a software package designed for fast and accurate alignment of NGS reads and specialized in identifying all mapping locations of each read. Hobbes2 efficiently identifies all mapping locations of reads using a novel technique that utilizes additional prefix q-grams to improve filtering. We extensively compare Hobbes2 with state-of-the-art read mappers, and show that Hobbes2 can be an order of magnitude faster than other read mappers while consuming less memory space and achieving similar accuracy. We propose Hobbes2 to improve the accuracy of read mapping, specialized in identifying all mapping locations of each read. Hobbes2 is implemented in C++, and the source code is freely available for download at http://hobbes.ics.uci.edu.
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