Name
Abstract | ||
|---|---|---|
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 . |
Year | DOI | Venue |
|---|---|---|
2015 | 10.1186/s12859-015-0557-5 | BMC Bioinformatics |
Keywords | Field | DocType |
microarrays,algorithms,bioinformatics | Genome,RNA,RNA-Seq,Biology,Context based,RNA splicing,Genome human,Bioinformatics,Mapping algorithm,Genetics,DNA microarray | Journal |
Volume | Issue | ISSN |
16 | 1 | 1471-2105 |
Citations | PageRank | References |
3 | 0.45 | 6 |
Authors | ||
5 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Thomas Bonfert | 1 | 3 | 0.45 |
| Evelyn Kirner | 2 | 3 | 0.45 |
| Gergely Csaba | 3 | 89 | 7.60 |
| Ralf Zimmer | 4 | 269 | 28.70 |
| Caroline C Friedel | 5 | 180 | 11.21 |