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

  • Enzo Rucci
  • Carlos Garcia
  • Guillermo Botella
  • Armando De Giusti
  • Marcelo Naiouf
  • Manuel Prieto-Matias
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10209)

Abstract

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.

Keywords

Field Programmable Gate Array Graphic Processor Unit Field Programmable Gate Array Implementation Latency Memory Access Dedicated Memory 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

This work has been partially supported by Spanish government through research contract TIN2015-65277-R and CAPAP-H5 network (TIN2014-53522).

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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Enzo Rucci
    • 1
  • Carlos Garcia
    • 2
  • Guillermo Botella
    • 2
  • Armando De Giusti
    • 1
  • Marcelo Naiouf
    • 3
  • Manuel Prieto-Matias
    • 2
  1. 1.III-LIDI, CONICET, Facultad de InformáticaUniversidad Nacional de La PlataLa PlataArgentina
  2. 2.Depto. Arquitectura de Computadores y AutomáticaUniversidad Complutense de MadridMadridSpain
  3. 3.III-LIDI, Facultad de InformáticaUniversidad Nacional de La PlataLa PlataArgentina

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