An FPGA-Based Seed Extension IP Core for BWA-MEM DNA Alignment

With the very fast improvements in technology, the amount of data in DNA alignment is exponential growth. Although there are more and more new DNA alignment algorithms proposed in the last decade to increase mapping performance, it still takes up to many days for aligning the whole human genome even with large clusters. In this work, we focus on one of the most time-consuming steps in the state-of-the-art DNA alignment algorithm, the seed extension in the BWA-MEM algorithm. We propose an FPGA-based IP core for the seed extension phase of the algorithm so that FPGA can be used to accelerate overall application performance. The core is designed in a pipeline model and technology-independent. Our core can be synthesized and implemented on various FPGA families with efficient hardware resources. The core can function at up to 243 MHz when implementfied on Xilinx Zynq FPGA device.

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