Re-alignment of the unmapped reads with base quality score

BMC Bioinformatics

Proceedings

Qianghua Xiao¹  Zhen Zhang¹  Jianxin Wang¹  Xiaoqing Peng¹  Min Li¹  Yi Pan² 

[1] School of Information Science and Engineering, Central South University, 410083, Changsha, China;School of Information Science and Engineering, Central South University, 410083, Changsha, China;Department of Computer Science, Georgia State University, 30302-4110, Atlanta, USA;

关键词: re-alignment;    unmapped reads;    base quality score;   

DOI  :  10.1186/1471-2105-16-S5-S8

来源: Springer

【 摘 要 】

MotivationBased on the next generation genome sequencing technologies, a variety of biological applications are developed, while alignment is the first step once the sequencing reads are obtained. In recent years, many software tools have been developed to efficiently and accurately align short reads to the reference genome. However, there are still many reads that can't be mapped to the reference genome, due to the exceeding of allowable mismatches. Moreover, besides the unmapped reads, the reads with low mapping qualities are also excluded from the downstream analysis, such as variance calling. If we can take advantages of the confident segments of these reads, not only can the alignment rates be improved, but also more information will be provided for the downstream analysis.ResultsThis paper proposes a method, called RAUR (Re-align the Unmapped Reads), to re-align the reads that can not be mapped by alignment tools. Firstly, it takes advantages of the base quality scores (reported by the sequencer) to figure out the most confident and informative segments of the unmapped reads by controlling the number of possible mismatches in the alignment. Then, combined with an alignment tool, RAUR re-align these segments of the reads. We run RAUR on both simulated data and real data with different read lengths. The results show that many reads which fail to be aligned by the most popular alignment tools (BWA and Bowtie2) can be correctly re-aligned by RAUR, with a similar Precision. Even compared with the BWA-MEM and the local mode of Bowtie2, which perform local alignment for long reads to improve the alignment rate, RAUR also shows advantages on the Alignment rate and Precision in some cases. Therefore, the trimming strategy used in RAUR is useful to improve the Alignment rate of alignment tools for the next-generation genome sequencing.AvailabilityAll source code are available at http://netlab.csu.edu.cn/bioinformatics/RAUR.html.

【 授权许可】

Unknown   
© Peng et al.; licensee BioMed Central Ltd. 2015. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.