BarraCUDA - a fast short read sequence aligner using graphics processing units.

ABSTRACT:

Background

With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence.

Findings

Using the NVIDIA Compute Unified Device Architecture (CUDA) software d

SUBMITTER: Klus P 

PROVIDER: S-EPMC3278344 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature