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How to accelerate genomic sequence alignment 4X using half an FPGA

Alexandre Cornu 1 Steven Derrien 2 Dominique Lavenier 1
1 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
2 CAIRN - Energy Efficient Computing ArchItectures with Embedded Reconfigurable Resources
Inria Rennes – Bretagne Atlantique , IRISA-D3 - ARCHITECTURE
Abstract : Designing FPGA-based accelerators is a difficult and time-consuming task that can be eased by High Level Synthesis Tools. To illustrate, we describe how a C-to-hardware methodology has been used to develop an efficient systolic array for the genomic sequence alignment problem. We also compare design performance with traditional HDL implementations.
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Contributor : Dominique Lavenier <>
Submitted on : Thursday, November 3, 2011 - 9:48:05 AM
Last modification on : Thursday, January 7, 2021 - 4:14:24 PM


  • HAL Id : hal-00637833, version 1


Alexandre Cornu, Steven Derrien, Dominique Lavenier. How to accelerate genomic sequence alignment 4X using half an FPGA. 2011. ⟨hal-00637833⟩



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