De novo fragment assembly with short mate-paired reads: Does the read length matter?
De novo fragment assembly with short mate-paired reads: Does the read length matter?
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DOI：
10.1101/gr.079053.108
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发表时间：
2009-02-01
期刊：
影响因子：
7
通讯作者：
Pevzner, Pavel A.
中科院分区：
文献类型：
--
作者：
Chaisson, Mark J.;Brinza, Dumitru;Pevzner, Pavel A.
目前，增加读段长度被视为下一代测序技术进行片段组装的关键条件。然而，引入配对读段（由长度的间隙GapLength分隔）开启了将短配对转化为长度接近GapLength的长配对读段的可能性，并且因此提出了关于读段长度（与GapLength相对）是否甚至重要的问题。我们描述了一种新的工具，EULER-USR，用于组装配对短读段，并使用它来分析读段长度是否重要的问题。我们进一步补充了正在进行的实验努力，以最大限度地增加有效读长的一种新的计算方法的读长。虽然通常的做法是修剪读段的易错尾部，但我们提出了一种使用重复图用纠错代替修剪的方法。该结果的一个重要且违反直觉的含义是，可以将随着长度“超过其引物”而降解的测序反应延伸到错误率增长超过片段组装通常可接受的水平的位置。
Increasing read length is currently viewed as the crucial condition for fragment assembly with next-generation sequencing technologies. However, introducing mate-paired reads (separated by a gap of length, GapLength) opens a possibility to transform short mate-pairs into long mate-reads of length approximate to GapLength, and thus raises the question as to whether the read length (as opposed to GapLength) even matters. We describe a new tool, EULER-USR, for assembling mate-paired short reads and use it to analyze the question of whether the read length matters. We further complement the ongoing experimental efforts to maximize read length by a new computational approach for increasing the effective read length. While the common practice is to trim the error-prone tails of the reads, we present an approach that substitutes trimming with error correction using repeat graphs. An important and counterintuitive implication of this result is that one may extend sequencing reactions that degrade with length "past their prime'' to where the error rate grows above what is normally acceptable for fragment assembly.