SNPRelate

"SNPRelate" is a sophisticated software tool developed to address the computational challenges associated with Genome-Wide Association Studies (GWAS), particularly in the analysis of SNP (Single Nucleotide Polymorphism) data. Designed to work efficiently on multi-core symmetric multiprocessing computer architectures, SNPRelate, along with its companion package gdsfmt, significantly accelerates two critical GWAS computations: Principal Component Analysis (PCA) and relatedness analysis via identity-by-descent measures.

The core algorithms of SNPRelate are written in C/C++ and have been highly optimized for speed and efficiency. Benchmarking tests reveal that SNPRelate's uniprocessor implementations of PCA and identity-by-descent analysis are substantially faster—approximately 8 to 50 times for PCA and up to 30 to 300 times faster for identity-by-descent analysis when utilizing eight cores—compared to those provided by popular tools such as EIGENSTRAT and PLINK.