An FPGA Based Accelerator of the Bi-Directional Wavefront Algorithm for Pairwise Sequence Alignment

Advances in next-generation sequencing technolo-gies have resulted in a prodigious amount of genomic sequence data. Harnessing the information encoded in a genome has far-reaching consequences and has been instrumental in assessing variability and evolutionary relationships between genomes. The first step in analysing genomic data consists of aligning reads against a reference genome. As these applications reach genome scale length, they incur a huge computational cost. Recently, the bi-directional wavefront alignment algorithm (Bi-WFA) has been introduced, which gives the best time and space complexity of sequence alignment till date. This paper presents a novel FPGA accelerator design which implements the breakthrough Bi-WFA algorithm and computes the sequence alignment. The design is implemented in VCUl18 Virtex Ultrascale+ FPGA board and makes use of several parallel modules to find junctions using Bi-WFA, achieving speedups of 4x to 6x compared to software implementation.