gdsfmt 1.4.0 / SNPRelate 0.9.19 – CoreArray Genomic Data Structure (GDS) R Interface / Parallel Computing Toolset for GWAS

gdsfmt 1.4.0 / SNPRelate 0.9.19

:: DESCRIPTION

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 ~8 to 50 times faster than the implementations provided by the popular EIGENSTRAT (v3.0) and PLINK (v1.07) programs respectively, and can be sped up to 30~300 folds by utilizing eight cores. SNPRelate can analyze tens of thousands of samples, with millions of SNPs.

::DEVELOPER

Xiuwen Zheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R
  • BioConductor

:: DOWNLOAD

  gdsfmt / SNPRelate

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Dec 1;28(24):3326-8. doi: 10.1093/bioinformatics/bts606. Epub 2012 Oct 11.
A high-performance computing toolset for relatedness and principal component analysis of SNP data.
Zheng X, Levine D, Shen J, Gogarten SM, Laurie C, Weir BS.