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

BMC Bioinformatics. 2015 Apr 17;16:122. doi: 10.1186/s12859-015-0557-5.


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 .

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Exons / genetics
  • Genome, Human*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • INDEL Mutation / genetics
  • RNA, Messenger / genetics*
  • Sequence Analysis, RNA / methods*
  • Transcriptome


  • RNA, Messenger