Reconfigurable Acceleration of Short Read Mapping with Biological Consideration

Abstract

Existing FPGA accelerators for short read mapping often fail to utilize the complete biological information in sequencing data for simple hardware design, leading to missed or incorrect alignment. Furthermore, their performance may not be optimized across hardware platforms. This paper proposes a novel alignment pipeline that considers all information in sequencing data for biologically accurate acceleration of short read mapping. To ensure the performance of the proposed design optimized across different platforms, we accelerate the memory-bound operations which have been a bottleneck in short read mapping. Specifically, we partition the FM-index into buckets. The length of each bucket is equal to an optimal multiple of the memory burst size and is determined through data-driven exploration. A tool has been developed to obtain the optimal parameters of the design for different hardware platforms to enhance performance optimization. Experimental results indicate that our design maximizes alignment accuracy compared to the state-of-the-art software Bowtie, mapping reads 4.48x as fast. Compared to the previous hardware aligner, our achieved accuracy is 97.7% which reports 4.48 M more valid alignments with a similar speed.