Improving transcriptome assembly through error correction of high-throughput sequence reads.
Improving transcriptome assembly through error correction of high-throughput sequence reads.
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作者：
Macmanes MD;Eisen MB
功能基因组学的研究，特别是在非模式生物中，在过去几年中通过使用转录组和RNAseq得到了显着改善。虽然这些研究可能非常强大，但这是一个计算密集型程序，必须完成参考转录组的从头构建，作为进一步分析的先决条件。准确的参考是至关重要的，因为所有下游步骤，包括估计转录本丰度，都严重依赖于准确参考的构建。虽然大量的研究已经做了组装，直到最近才有预组装程序进行了详细的研究。具体而言，已经报道了几种独立的纠错模块，虽然它们已经显示出在测序读数水平上有效地减少错误，但纠错如何影响组装准确性在很大程度上是未知的。在这里，我们通过使用模拟和经验数据集显示，对测序读数应用纠错对组装准确性具有显著的积极影响，并且应该应用于所有数据集。一个完整的命令集合，将允许产生爬行动物纠正读取可在和作为文件S1。
The study of functional genomics, particularly in non-model organisms, has been dramatically improved over the last few years by the use of transcriptomes and RNAseq. While these studies are potentially extremely powerful, a computationally intensive procedure, the de novo construction of a reference transcriptome must be completed as a prerequisite to further analyses. The accurate reference is critically important as all downstream steps, including estimating transcript abundance are critically dependent on the construction of an accurate reference. Though a substantial amount of research has been done on assembly, only recently have the pre-assembly procedures been studied in detail. Specifically, several stand-alone error correction modules have been reported on and, while they have shown to be effective in reducing errors at the level of sequencing reads, how error correction impacts assembly accuracy is largely unknown. Here, we show via use of a simulated and empiric dataset, that applying error correction to sequencing reads has significant positive effects on assembly accuracy, and should be applied to all datasets. A complete collection of commands which will allow for the production of Reptile corrected reads is available at and as File S1.
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DOI：
10.2202/1544-6115.1627
发表时间：
2011-01-01
影响因子：
0.9
作者：
Auer, Paul L.;Doerge, Rebecca W.
通讯作者：
Doerge, Rebecca W.
DOI：
10.1093/dnares/dss036
发表时间：
2013-02
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Muñoz-Mérida A;González-Plaza JJ;Cañada A;Blanco AM;García-López Mdel C;Rodríguez JM;Pedrola L;Sicardo MD;Hernández ML;De la Rosa R;Belaj A;Gil-Borja M;Luque F;Martínez-Rivas JM;Pisano DG;Trelles O;Valpuesta V;Beuzón CR
通讯作者：
Beuzón CR
影响因子：
12.3
作者：
Kelley DR;Schatz MC;Salzberg SL
通讯作者：
Salzberg SL
影响因子：
48
作者：
Mortazavi, Ali;Williams, Brian A.;Wold, Barbara
通讯作者：
Wold, Barbara
影响因子：
3
作者：
Cox MP;Peterson DA;Biggs PJ
通讯作者：
Biggs PJ