TY - JOUR T1 - Concurrent and Accurate Short Read Mapping on Multicore Processors. JF - IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM Y1 - 2015 A1 - Martinez, Hector A1 - Tárraga, Joaquín A1 - Medina, Ignacio A1 - Barrachina, Sergio A1 - Castillo, Maribel A1 - Dopazo, Joaquin A1 - Quintana-Orti, Enrique S KW - HPC KW - NGS KW - short real mapping AB - 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, [Formula: see text] ([Formula: see text] is an open-source application. The software is available at http://www.opencb.org, 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 [Formula: see text], 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. VL - 12 UR - http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=7010005 ER -