ContextMap 2 – fast and accurate context-based RNA-Seq mapping

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.

Here, researchers from Ludwig-Maximilians-Universität München 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.


The researchers 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.

Availability – ContextMap 2 is freely available at

Bonfert T, Kirner E, Csaba G, Zimmer R, Friedel CC. (2015) ContextMap 2: fast and accurate context-based RNA-seq mapping. BMC Bioinformatics 16:122. [abstract]

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