MinimapPool: an improved flexible and efficient parallel algorithm based on minimap2

Third-generation sequencing techniques have achieved major breakthroughs in sequencing long reads and speed. Continuous improvements in sequencing techniques have reduced sequencing costs, and the number of sequencing data files has shown explosive growth. In terms of sequence alignment, to deal with these high numbers and large-scale data, the conventional serial alignment method can no longer effectively meet the research requirements, therefore, it is of great importance to develop a faster, low-load, and compatible parallel alignment program. In this paper, we propose a parallel task pool algorithm based on the minimap2, a sequence alignment tool, and develop the task pool parallel alignment program based on this algorithm. We compare the program’s work with the average segmentation parallel alignment program. The results show that the task pool parallel alignment program has significant improvement in speedup, memory load, segmentation flexibility, and computational efficiency, it also has good scalability and computational stability. MinimapPool is available at https://github.com/krkrcc/MinimapPool.