ContextMap 2: fast and accurate context-based RNA-seq mapping.
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 .
Institute for Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, Munich, 80333, Germany. thomas.bonfert@bio.ifi.lmu.de.
Thomas
T
Bonfert
Institute for Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, Munich, 80333, Germany. evelyn.kirner@campus.lmu.de.
Evelyn
E
Kirner
Institute for Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, Munich, 80333, Germany. gergely.csaba@bio.ifi.lmu.de.
Gergely
G
Csaba
Institute for Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, Munich, 80333, Germany. ralf.zimmer@bio.ifi.lmu.de.
Ralf
R
Zimmer
Institute for Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, Munich, 80333, Germany. caroline.friedel@bio.ifi.lmu.de.
Caroline C
CC
Friedel
D000465:Algorithms; D005091:Exons / Q000235:genetics; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D054643:INDEL Mutation / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome
D012333:RNA, Messenger