@article {10, title = {Concurrent and Accurate Short Read Mapping on Multicore Processors.}, journal = {IEEE/ACM Trans Comput Biol Bioinform}, volume = {12}, year = {2015}, month = {2015 Sep-Oct}, pages = {995-1007}, abstract = {

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 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 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.

}, issn = {1557-9964}, doi = {10.1109/TCBB.2015.2392077}, author = {Mart{\'\i}nez, H{\'e}ctor and Tarraga, Joaquin and Medina, Ignacio and Barrachina, Sergio and Castillo, Maribel and Dopazo, Joaqu{\'\i}n and Quintana-Ort{\'\i}, Enrique S} }