异构计算平台上高效加速基因组短读映射

Ernst Houtgast, V. Sima, G. Marchiori, K. Bertels, Z. Al-Ars
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引用次数: 6

摘要

我们提出了一种新的fpga加速BWA-MEM实现,这是一种流行的基因组数据制图工具。将单个Xilinx Virtex-7 Alpha Data外接卡上的FPGA实现的性能和功耗与纯软件基准系统进行了比较。通过将Seed Extension阶段卸载到FPGA上,实现了整体应用级性能的两倍加速和1.6倍的功率效率增益。为了方便与平台和工具无关的比较,引入了每焦耳单位的碱基对作为功率效率的度量。FPGA设计能够每焦耳映射多达34000个碱基对。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Power-Efficient Accelerated Genomic Short Read Mapping on Heterogeneous Computing Platforms
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.
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