@article {Srivastava029652, author = {Avi Srivastava and Hirak Sarkar and Nitish Gupta and Rob Patro}, title = {RapMap: A Rapid, Sensitive and Accurate Tool for Mapping RNA-seq Reads to Transcriptomes}, elocation-id = {029652}, year = {2016}, doi = {10.1101/029652}, publisher = {Cold Spring Harbor Laboratory}, 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 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{\textemdash} our tool implementing quasi-mapping{\textemdash} is capable of mapping sequencing reads to a target transcriptome substantially faster than existing alignment tools. The algorithm we employ 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.Availability: RapMap is implemented in C++11 and is available as open-source software, under GPL v3, at https://github.com/COMBINE-lab/RapMap.Contact: rob.patro{at}cs.stonybrook.edu}, URL = {https://www.biorxiv.org/content/early/2016/01/16/029652}, eprint = {https://www.biorxiv.org/content/early/2016/01/16/029652.full.pdf}, journal = {bioRxiv} }