RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes.
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.



We introduce a novel concept, quasi-mapping, and an efficient algorithm implementing this approach 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-our tool implementing quasi-mapping-is capable of mapping sequencing reads to a target transcriptome substantially faster than existing alignment tools. The algorithm we use to implement quasi-mapping 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. We demonstrate how quasi-mapping can be successfully applied to the problems of transcript-level quantification from RNA-seq reads and the clustering of contigs from de novo assembled transcriptomes into biologically meaningful groups.



RapMap is implemented in C ++11 and is available as open-source software, under GPL v3, at https://github.com/COMBINE-lab/RapMap



rob.patro@cs.stonybrook.edu



Supplementary data are available at Bioinformatics online.
Department of Computer Science, Stony Brook University Stony Brook, New York, NY 11794-2424, USA.
Avi
A
Srivastava
Department of Computer Science, Stony Brook University Stony Brook, New York, NY 11794-2424, USA.
Hirak
H
Sarkar
Department of Computer Science, Stony Brook University Stony Brook, New York, NY 11794-2424, USA.
Nitish
N
Gupta
Department of Computer Science, Stony Brook University Stony Brook, New York, NY 11794-2424, USA.
Rob
R
Patro
D000465:Algorithms; D012313:RNA; D017423:Sequence Analysis, RNA; D012984:Software; D059467:Transcriptome
D012313:RNA