Introduction

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.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.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 .

Publications

  1. ContextMap 2: fast and accurate context-based RNA-seq mapping.
    Cite this
    Bonfert T, Kirner E, Csaba G, Zimmer R, Friedel CC, 2015-04-01 - BMC Bioinformatics

Credits

  1. Thomas Bonfert
    Developer

    Institute for Informatics, Ludwig-Maximilians-Universität München

  2. Evelyn Kirner
    Developer

    Institute for Informatics, Ludwig-Maximilians-Universität München

  3. Gergely Csaba
    Developer

    Institute for Informatics, Ludwig-Maximilians-Universität München

  4. Ralf Zimmer
    Developer

    Institute for Informatics, Ludwig-Maximilians-Universität München

  5. Caroline C Friedel
    Investigator

    Institute for Informatics, Ludwig-Maximilians-Universität München

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Summary
AccessionBT006548
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByCaroline C Friedel