The explosion of Next Generation Sequencing (NGS) data with over one billion reads per day poses a great challenge to the capability of current computing systems. In this paper, we proposed a CPU-FPGA heterogeneous architecture for accelerating a short reads mapping algorithm, which was built upon the concept of hash-index. In particular, by extracting and mapping the most time-consuming and basic operations to specialized processing elements (PEs), our new algorithm is favorable to efficient acceleration on FPGAs. The proposed architecture is implemented and evaluated on a customized FPGA accelerator card with a Xilinx Virtex5 LX330 FPGA resided. Limited by available data transfer bandwidth, our NGS mapping accelerator, which operates at 175MHz, integrates up to 100 PEs. Compared to an Intel six-cores CPU, the speedup of our accelerator ranges from 22.2 times to 42.9 times.
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