GenSeq+: A Scalable High-Performance Accelerator for Genome Sequencing.

Abstract

Genome sequencing is one of the most challenging problems in computational biology and bioinformatics. As a traditional algorithm, the string match meets a challenge with the development of the massive volume of data because 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. As a classic fast and exact single pattern matching algorithm, Knuth-Morris-Pratt (KMP) algorithm has been demonstrated in network security and computational biology. However, with the increasing amount of data in the modern society, it becomes increasingly important and essential to provide a High-performance implementation of KMP algorithm. In this article, we implement a scalable KMP accelerator based on FPGA, named GeneKMP. The accelerator is composed of different computing units to achieve a pipelined organization for higher throughput with satisfying scalability. A novel programming model is provided to alleviate the burden of the high-level programmers. We provide a greedy-based partitioning algorithm for the software/hardware design paradigms. Experimental results on the state-of-the-art Xilinx FPGA hardware prototype show that our accelerator can achieve up to a promising speedup with insignificant hardware cost and power consumption.