Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA

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 prese...

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Detalles Bibliográficos
Autores principales: Rucci, Enzo, García Sanchez, Carlos, Botella, Guillermo, De Giusti, Armando Eduardo, Naiouf, Marcelo, Prieto-Matias, Manuel
Formato: Objeto de conferencia
Lenguaje:Inglés
Publicado: 2017
Materias:
Ciencias Informáticas
Field Programmable Gate Array
Graphic Processor Unit
Field Programmable Gate Array Implementation
Latency Memory Access
Dedicated Memory
Acceso en línea:http://sedici.unlp.edu.ar/handle/10915/82872
Aporte de:
SEDICI (UNLP) de Universidad Nacional de La Plata
Descripción
Sumario: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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