BSAlign: a library for nucleotide sequence alignment

Abstract

Increasing the accuracy of the nucleotide sequence alignment is an essential issue in genomics research. Although classic dynamic-programming algorithms (e.g., Smith-Waterman and Needleman-Wunsch) guarantee to produce the optimal result, their time complexity hinders the application of large-scale sequence alignment. Many optimization efforts that aim to accelerate the alignment process generally come from three perspectives: re-designing data structures (e.g., diagonal or striped Single Instruction Multiple Data (SIMD) implementations), increasing the number of parallelisms in SIMD operations (e.g., difference recurrence relation), or reducing searching space (e.g., banded dynamic programming). However, no methods combine all these three aspects to build an ultra-fast algorithm. We have developed a Banded Striped Aligner(library) named BSAlign that delivers accurate alignment results at an ultra-fast speed by knitting a series of novel methods together to take advantage of all of the aforementioned three perspectives with highlights such as active F-loop in striped vectorization and striped move in banded dynamic programming. We applied our new acceleration design on both regular and edit-distance pairwise alignment. BSAlign achieved 2-fold speed-up than other SIMD based implementations for regular pairwise alignment, and 1.5 to 4-fold speedup in edit distance based implementations for long reads. BSAlign is implemented in C programing language and is available at https://github.com/ruanjue/bsalign.