通过多次比对纠正短读中的错误。

Correcting errors in short reads by multiple alignments.

机构信息

Department of Computer Science, Helsinki Institute for Information Technology HIIT, University of Helsinki, Helsinki, Finland.

出版信息

Bioinformatics. 2011 Jun 1;27(11):1455-61. doi: 10.1093/bioinformatics/btr170. Epub 2011 Apr 5.

DOI:10.1093/bioinformatics/btr170

PMID:21471014

Abstract

MOTIVATION

Current sequencing technologies produce a large number of erroneous reads. The sequencing errors present a major challenge in utilizing the data in de novo sequencing projects as assemblers have difficulties in dealing with errors.

RESULTS

We present Coral which corrects sequencing errors by forming multiple alignments. Unlike previous tools for error correction, Coral can utilize also bases distant from the error in the correction process because the whole read is present in the alignment. Coral is easily adjustable to reads produced by different sequencing technologies like Illumina Genome Analyzer and Roche/454 Life Sciences sequencing platforms because the sequencing error model can be defined by the user. We show that our method is able to reduce the error rate of reads more than previous methods.

AVAILABILITY

The source code of Coral is freely available at http://www.cs.helsinki.fi/u/lmsalmel/coral/.

摘要

动机

当前的测序技术会产生大量错误的读取。测序错误在从头测序项目中利用数据时带来了重大挑战，因为组装器难以处理错误。

结果

我们提出了 Coral，它通过形成多个比对来纠正测序错误。与以前用于纠错的工具不同，Coral 可以在纠错过程中利用远离错误的碱基，因为整个读取都存在于比对中。Coral 可以轻松地调整到不同测序技术产生的读取，如 Illumina Genome Analyzer 和 Roche/454 Life Sciences 测序平台，因为用户可以定义测序错误模型。我们表明，我们的方法能够比以前的方法更有效地降低读取错误率。