Porting and Optimizing SOAP2 on Loongson Architecture

SOAP2 is a high precision, high performance and high efficiency alignment tool which is developed by the Beijing Genomics Institute. SOAP2 has become one of the mainstream biological sequence alignment software. However, SOAP2 is developed for X86 architecture, so we port and optimize SOAP2 to Loongson platform. Firstly, we make SOAP2 to be able to run on Loongson machine correctly. Second, its speed, sensitivity and hits of result are improved. This paper has comprehensively conducted a transplantation and optimization of SOAP2 in many aspects including using Loongson multimedia instructions, using thread pool and a new algorithm proposed by this paper on Loongson platform. We tested it on human chromosome 1 and found that optimized SOAP2 not only reduced memory overhead but also improved alignment speed by about 55%, sensitivity from about 66.8% to about 77% and always reported more mapped reads and occurrences. At the same time, in the process of optimization, this paper also proposes a method for applying Loongson multimedia instructions more efficiently. This provides a new guidance for software transplantation and optimization on Loongson platform.