Accelerating Smith-Waterman alignment of long DNA sequences with OpenCL on FPGA
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ArticleDescription: 1 archivo (703,6 kB)Subject(s): Online resources: Summary: With the greater importance of parallel architectures such as GPUs or Xeon Phi accelerators, the scientific community has developed efficient solutions in the bioinformatics field. In this context, FPGAs begin to stand out as high performance devices with moderate power consumption. This paper presents and evaluates a parallel strategy of the well-known Smith-Waterman algorithm using OpenCL on Intel/Altera’s FPGA for long DNA sequences. We efficiently exploit data and pipeline parallelism on a Intel/Altera Stratix V FPGA reaching upto 114 GCUPS in less than 25 watt power requirements.
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Biblioteca de la Facultad de Informática | Biblioteca digital | A0918 (Browse shelf(Opens below)) | Link to resource | Recurso en Línea |
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With the greater importance of parallel architectures such as GPUs or Xeon Phi accelerators, the scientific community has developed efficient solutions in the bioinformatics field. In this context, FPGAs begin to stand out as high performance devices with moderate power consumption. This paper presents and evaluates a parallel strategy of the well-known Smith-Waterman algorithm using OpenCL on Intel/Altera’s FPGA for long DNA sequences. We efficiently exploit data and pipeline parallelism on a Intel/Altera Stratix V FPGA reaching upto 114 GCUPS in less than 25 watt power requirements.
IWBBIO 2017. International Conference on Bioinformatics and Biomedical Engineering (2017 : Granada, España)