The Smith-Waterman algorithm is widely used in bioinformatics and is often used as a benchmark of FPGA performance. Here we present our highly optimized Smith- Waterman implementation on Intel FPGAs using OpenCL.
Our implementation is both faster and more efficient than other current Smith-Waterman implementations, obtaining a theoretical performance of 214 GCUPS. Moreover, due to the streaming, implicit synchronizing nature of our implementation, which streams alignments and places no restrictions on
the number of alignments in flight, it achieves 99.8% of this performance in practice, almost three times as fast as previous implementations. The expressiveness of OpenCL results in a significant reduction in lines of code, and in a significant reduction of development time compared to programming in
regular hardware description languages.
Original languageEnglish
Title of host publication2017 IEEE 17th International Conference on BioInformatics and BioEngineering (BIBE)
Place of PublicationPiscataway
Number of pages5
ISBN (Electronic)978-1-5386-1324-5
ISBN (Print)978-1-5386-1325-2
Publication statusPublished - 2017
EventBIBE 2017: 17th IEEE International Conference on BioInformatics and BioEngineering - Washington DC, United States
Duration: 23 Oct 201725 Oct 2017


ConferenceBIBE 2017
Abbreviated titleBIBE 2017
CountryUnited States
CityWashington DC
Internet address

    Research areas

  • FPGA, OpenCL, Smith-Waterman, systolic array

ID: 30800136