Concurrent and Accurate Short Read Mapping on Multicore Processors.

TitleConcurrent and Accurate Short Read Mapping on Multicore Processors.
Publication TypeJournal Article
Year of Publication2015
AuthorsMartínez H, Tarraga J, Medina I, Barrachina S, Castillo M, Dopazo J, Quintana-Ortí ES
JournalIEEE/ACM Trans Comput Biol Bioinform
Date Published2015 Sep-Oct

We introduce a parallel aligner with a work-flow organization for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, HPG Aligner SA (HPG Aligner SA is an open-source application. The software is available at, exploits a suffix array to rapidly map a large fraction of the RNA fragments (reads), as well as leverages the accuracy of the Smith-Waterman algorithm to deal with conflictive reads. The aligner is enhanced with a careful strategy to detect splice junctions based on an adaptive division of RNA reads into small segments (or seeds), which are then mapped onto a number of candidate alignment locations, providing crucial information for the successful alignment of the complete reads. The experimental results on a platform with Intel multicore technology report the parallel performance of HPG Aligner SA, on RNA reads of 100-400 nucleotides, which excels in execution time/sensitivity to state-of-the-art aligners such as TopHat 2+Bowtie 2, MapSplice, and STAR.