Parallel and Scalable Short-Read Alignment on Multi-Core Clusters Using UPC+.

ABSTRACT: The growth of next-generation sequencing (NGS) datasets poses a challenge to the alignment of reads to reference genomes in terms of alignment quality and execution speed. Some available aligners have been shown to obtain high quality mappings at the expense of long execution times. Finding fast yet accurate software solutions is of high importance to research, since availability and size of NGS datasets continue to increase. In this work we present an efficient parallelization approach for NGS short-read alignment on multi-core clusters. Our approach takes advantage of a distributed shared memory programming model based on the new UPC++ language. Experimental results using the CUSHAW3 aligner show that our implementation based on dynamic scheduling obtains good scalability on multi-core c

SUBMITTER: Gonzalez-Dominguez J 

PROVIDER: S-EPMC4711716 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature