ContextMap 2: fast and accurate context-based RNA-seq mapping

被引:40
作者
Bonfert, Thomas [1 ]
Kirner, Evelyn [1 ]
Csaba, Gergely [1 ]
Zimmer, Ralf [1 ]
Friedel, Caroline C. [1 ]
机构
[1] Univ Munich, Inst Informat, D-80333 Munich, Germany
关键词
READ ALIGNMENT;
D O I
10.1186/s12859-015-0557-5
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Background: Mapping of short sequencing reads is a crucial step in the analysis of RNA sequencing (RNA-seq) data. ContextMap is an RNA-seq mapping algorithm that uses a context-based approach to identify the best alignment for each read and allows parallel mapping against several reference genomes. Results: In this article, we present ContextMap 2, a new and improved version of ContextMap. Its key novel features are: (i) a plug-in structure that allows easily integrating novel short read alignment programs with improved accuracy and runtime; (ii) context-based identification of insertions and deletions (indels); (iii) mapping of reads spanning an arbitrary number of exons and indels. ContextMap 2 using Bowtie, Bowtie 2 or BWA was evaluated on both simulated and real-life data from the recently published RGASP study. Conclusions: We show that ContextMap 2 generally combines similar or higher recall compared to other state-of-the-art approaches with significantly higher precision in read placement and junction and indel prediction. Furthermore, runtime was significantly lower than for the best competing approaches. ContextMap 2 is freely available at http://www.bio.ifi.lmu.de/ContextMap.
引用
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页数:15
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