RT Journal Article
SR Electronic
T1 RapMap: A Rapid, Sensitive and Accurate Tool for Mapping RNA-seq Reads to Transcriptomes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 029652
DO 10.1101/029652
A1 Avi Srivastava
A1 Hirak Sarkar
A1 Rob Patro
YR 2015
UL http://biorxiv.org/content/early/2015/10/22/029652.abstract
AB 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, quasimapping, 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-mapping algorithm — is capable of mapping sequencing reads to a target transcriptome substantially faster than existing alignment tools. The quasimapping 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, under GPL v3, at https://github.com/COMBINE-lab/RapMap.