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, HPG Aligner SA (HPG Aligner SA is an open-source application. The software is available at http://www.opencb.org/), exploits a suf...

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Bibliographic Details
Published in:IEEE/ACM transactions on computational biology and bioinformatics 2015-09, Vol.12 (5), p.995-1007
Main Authors: Martinez, Hector, Tarraga, Joaquin, Medina, Ignacio, Barrachina, Sergio, Castillo, Maribel, Dopazo, Joaquin, Quintana-Orti, Enrique S.
Format: Article
Language:English
Subjects:
Alignment
Base Sequence
Bioinformatics
Chromosome Mapping - instrumentation
Chromosome Mapping - methods
Computational biology
Computer programs
Equipment Design
Equipment Failure Analysis
Genomics
high performance computing
High-Throughput Nucleotide Sequencing - instrumentation
High-Throughput Nucleotide Sequencing - methods
Mapping
Microprocessors
Molecular Sequence Data
multicore processors
Portable document format
Processors
Reproducibility of Results
Ribonucleic acids
RNA
RNA - genetics
Sensitivity
Sensitivity and Specificity
Sequence Alignment - instrumentation
Sequence Alignment - methods
Sequence Analysis, RNA - instrumentation
Sequence Analysis, RNA - methods
Short-read alignment
Signal Processing, Computer-Assisted - instrumentation
Smith-Waterman's algorithm
Software
suffix array search
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Summary: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:1545-5963
1557-9964
DOI:10.1109/TCBB.2015.2392077