Concurrent and Accurate Short Read Mapping on Multicore Processors.

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, \sfHPG\; Aligner\; SA <alternatives><inline-graphic xlink:type="simple" xlink:href="barrachina-ieq1-2392077.gif"/></alternatives> (\sfHPG\; Aligner\; SA is an open-source application. The software is available at <uri xlink:type="simple">http://www.opencb.org/</uri>), 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 \sfHPG\; Aligner\; SA<alternatives> <inline-graphic xlink:type="simple" xlink:href="barrachina-ieq2-2392077.gif"/></alternatives>, 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. [ABSTRACT FROM PUBLISHER]