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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...
In this paper, we introduce an automated interconnect design strategy to create an efficient custom interconnect for kernels in an FPGA-based accelerator system to accelerate their communication behavior. Our custom interconnect includes an NoC, shared local memory solution or both. Depending on the quantitative communication profiling of the application, the interconnect is built using our proposed...
The Smith-Waterman (SW) algorithm is the only optimal local sequence alignment algorithm. There are many SW implementations on FPGA, which show speedups of up to 100x as compared to a general-purpose-processor (GPP). In this paper, we propose a design of the SW traceback, which is done in parallel with the matrix fill stage and which gives the optimal alignment after once scanning through the whole...
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