Dataset Information

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

ABSTRACT:

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 .

SUBMITTER: Bonfert T

PROVIDER: S-EPMC4411664 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature

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Publications

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

Bonfert Thomas T Kirner Evelyn E Csaba Gergely G Zimmer Ralf R Friedel Caroline C CC

BMC bioinformatics 20150417

<h4>Background</h4>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.<h4>Results</h4>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 ...[more]

PMID: 25928589

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Dataset Information

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

Background

Results

Conclusions

Publications

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

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