DOI

We propose a novel FPGA-accelerated BWA-MEM implementation, a popular tool for genomic data mapping. The performance and power-efficiency of the FPGA implementation on the single Xilinx Virtex-7 Alpha Data add-in card is compared
against a software-only baseline system. By offloading the Seed Extension phase onto the FPGA, a two-fold speedup in overall application-level performance is achieved and a 1.6x gain in power-efficiency. To facilitate platform and tool-agnostic comparisons, the base pairs per Joule unit is introduced as a measure of power-efficiency. The FPGA design is able to map up to 34 thousand base pairs per Joule.
Original languageEnglish
Pages1-1
Number of pages1
DOIs
Publication statusPublished - 2016
Event24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016 - Washington DC, United States
Duration: 1 May 20163 May 2016

Conference

Conference24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016
Abbreviated titleFCCM 2016
CountryUnited States
CityWashington DC
Period1/05/163/05/16

    Research areas

  • read mapping, FPGA, power-efficiency

ID: 10680867