Oct 22, 2015

RapMap: A Rapid, Sensitive and Accurate Tool for Mapping RNA-seq Reads to Transcriptomes

BioRxiv : the Preprint Server for Biology
Avi SrivastavaNitish Gupta

Abstract

Motivation: The alignment of sequencing reads to a transcriptome is a common and important step in many RNA-seq analysis tasks. When aligning RNA-seq reads directly to a transcriptome (as is common in the de novo setting or when a trusted reference annotation is available), care must be taken to report the potentially large number of multi-mapping locations per read. This can pose a substantial computational burden for existing aligners, and can considerably slow downstream analysis. Results: We introduce a novel algorithm, quasi-mappin, for mapping sequencing reads to a transcriptome. By attempting only to report the potential loci of origin of a sequencing read, and not the base-to-base alignment by which it derives from the reference, RapMap \---| the tool implementing this quasi-mappin algorithm \---| is capable of mapping sequencing reads to a target transcriptome substantially faster than existing alignment tools. The quasi-mapping algorithm itself uses several efficient data structures and takes advantage of the special structure of shared sequence prevalent in transcriptomes to rapidly provide highly-accurate mapping information. Availability: RapMap is implemented in C++11 and is available as open-source software, unde...Continue Reading

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Mentioned in this Paper

Computer Software
Nucleic Acid Sequencing
Patient Care
carbon-11 acetate
Sequencing
Sequence Analysis, RNA
Structure
Location
Mapping, Vessel
Analysis

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