title: Concurrent and Accurate Short Read Mapping on Multicore Processors.
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.
authors.forename: Héctor
authors.initials: H
authors.lastname: Martínez
authors.forename: Joaquín
authors.initials: J
authors.lastname: Tárraga
authors.forename: Ignacio
authors.initials: I
authors.lastname: Medina
authors.forename: Sergio
authors.initials: S
authors.lastname: Barrachina
authors.forename: Maribel
authors.initials: M
authors.lastname: Castillo
authors.forename: Joaquín
authors.initials: J
authors.lastname: Dopazo
authors.forename: Enrique S
authors.initials: ES
authors.lastname: Quintana-Ortí
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping / Q000295:instrumentation* / Q000379:methods; D004867:Equipment Design; D019544:Equipment Failure Analysis; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation* / Q000379:methods; D008969:Molecular Sequence Data; D012313:RNA / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000295:instrumentation / Q000379:methods; D017423:Sequence Analysis, RNA / Q000295:instrumentation* / Q000379:methods; D012815:Signal Processing, Computer-Assisted / Q000295:instrumentation*; D012984:Software
chemical_list: D012313:RNA