SNPRelate and gdsfmt - R package for NGS and GWAS

gdsfmt and SNPRelate are high-performance computing R packages for multi-core symmetric multiprocessing computer architectures. They are used to accelerate two key computations is GWAS: principal component analysis (PCA) and relatedness analysis using identity-by-descent (IBD) measures. The kernels of our algorithms are written in C/C++, and have been highly optimized. Benchmarks show the uniprocessor implementations of PCA and IBD are ~10 to 45 times faster than the implementations provided by the popular EIGENSTRAT (v3.0) and PLINK (v1.07) programs respectively, and can be sped up to 70~250 folds by utilizing eight cores. SNPRelate can analyze tens of thousands of samples, with millions of SNPs.

http://corearray.sourceforge.net/tutorials/SNPRelate/