Optimizations of Sequence Alignment on FPGA: A Case Study of Extended Sequence Alignment (Abstact Only)

Detecting similarities between sequences is an important part of Bioinformatics. In this poster, we explore the use of high-level synthesis tool and a field-programmable gate array (FPGA) for optimizing a sequence alignment algorithm. We demonstrate the optimization techniques to improve the performance of the extended sequence alignment algorithm in the BWA software package, a tool for mapping DNA sequences against a large reference sequence. Applying the optimizations to the algorithm using Xilinx SDAccel OpenCL-to-FPGA tool, we reduce the kernel execution time from 62.8 ms to 0.45 ms while the power consumption is approximately 11 Watts on the ADM-PCIE-8K5 FPGA platform.