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

id	I19-R120-10915-82872
record_format	dspace
institution	Universidad Nacional de La Plata
institution_str	I-19
repository_str	R-120
collection	SEDICI (UNLP)
language	Inglés
topic	Ciencias Informáticas Field Programmable Gate Array Graphic Processor Unit Field Programmable Gate Array Implementation Latency Memory Access Dedicated Memory
spellingShingle	Ciencias Informáticas Field Programmable Gate Array Graphic Processor Unit Field Programmable Gate Array Implementation Latency Memory Access Dedicated Memory Rucci, Enzo García Sanchez, Carlos Botella, Guillermo De Giusti, Armando Eduardo Naiouf, Marcelo Prieto-Matias, Manuel Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA
topic_facet	Ciencias Informáticas Field Programmable Gate Array Graphic Processor Unit Field Programmable Gate Array Implementation Latency Memory Access Dedicated Memory
description	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.
format	Objeto de conferencia Objeto de conferencia
author	Rucci, Enzo García Sanchez, Carlos Botella, Guillermo De Giusti, Armando Eduardo Naiouf, Marcelo Prieto-Matias, Manuel
author_facet	Rucci, Enzo García Sanchez, Carlos Botella, Guillermo De Giusti, Armando Eduardo Naiouf, Marcelo Prieto-Matias, Manuel
author_sort	Rucci, Enzo
title	Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA
title_short	Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA
title_full	Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA
title_fullStr	Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA
title_full_unstemmed	Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA
title_sort	accelerating smith-waterman alignment of long dna sequences with opencl on fpga
publishDate	2017
url	http://sedici.unlp.edu.ar/handle/10915/82872
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bdutipo_str	Repositorios
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Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA

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