Aligning sequencing reads to a reference genome is often essential in many comparative genomics pipelines. With the maturation of next-generation DNA sequencing (NGS) technologies, an enormous amount of sequence data ...
详细信息
ISBN:
(纸本)9781479989386
Aligning sequencing reads to a reference genome is often essential in many comparative genomics pipelines. With the maturation of next-generation DNA sequencing (NGS) technologies, an enormous amount of sequence data has been generated, this calls for the development of faster readalignment programs. In this paper we present an OpenCL implementation of the shortread aligner BarraCUDA [1], which is based on BWA software package [2] and utilises NVIDIAs GPGPU implementation, namely Compute Unified Device Architecture (CUDA) to parallelise the alignment of sequence reads. We re-implemented BarraCUDA aligner in OpenCL and test it on Intel's MIC architecture device - Xeon Phi 5110P coprocessor. Experiment results show that our OpenCL aligner performs better than its CPU-based software counterpart, with a 4 times performance boost compared to 8-thread BWA.
暂无评论