WFA-vect: a SIMD wavefront algorithm for gap-affine pairwise alignment

Sequence alignment is the core of many bioinformatics tasks such as read mapping, genome assembly, variant detection and so on. With the advent of the third generation sequencing, classical dynamic programming-based alignment algorithms face challenges in efficiently handling these long reads. To address this issue, we present WFA-vect, a SIMD-based fast sequence alignment algorithm based on WFA. In WFA-vect, we introduce load synchronous and mask-based branch strategies to make the algorithm more suitable for vectorization. The load synchronous equalizes the load across different vector units to facilitate vectorization. The mask-based branch uses branch masking to bypass branch, avoiding pipeline hazards. To avoid binding the SIMD algorithm to specific hardware, we design a universal vectorization framework, which allows researchers to quickly port WFA-vect to other platforms without needing to understand the details of the algorithm. WFA-vect attains a peak speedup of 3.87× and 3.98× for data with error rates of 1% and 20%, respectively, compared to the scalar algorithm, while maintaining the alignment result consistent. The code and documentation of WFA-vect are publicly available at https://github.com/nudt-bioinfo/WFA-vect.