GenServ: Genome Sequencing Services on Scalable Energy Efficient Accelerators

Abstract

As a traditional algorithm, the string match meets a challenge with the development of the massive volume of data be-cause of gene sequencing. Surveys show that there will be a huge amount of short read segments during the process of gene sequencing and the need for a highly efficient is urgent. The BWA is an effective algorithm to deal with the short read mapping. Compared with other short read mapping algorithms, the BWA algorithm has a smaller size, and this does not influence its effect. However, there is still not a system is used to accelerate the BWA algorithm especially. Thus we decide to build a system to expedite the algorithm and make it satisfied with the application of gene sequencing. In this paper, we present genome sequencing services on scalable energy-efficient accelerators. Especially, we first in-troduce the BWA algorithm and claim the reason for the choice of the algorithm. Then, we implement an accelerator based on FPGA to improve the performance of the algorithm. Com-pared to the other major platforms in accelerating the algo-rithm, we discuss the advantages of the FPGA platform and the limit of the other platform. Last, we build our hardware platform with a Xilinx ZYNQ FPGA development board, and the result shows that our accelerator can achieve a promising speedup and resource utilization and make it balanced be-tween power and cost.