An 'alpha' version of FlashPCA 2.0 is available at
https://github.com/gabraham/flashpca/tree/Spectra_online
This release
- Makes use of the Spectra eigen-decomposition library
(
https://github.com/yixuan/spectra/), replacing the previous
randomised algorithm
- Is substantially faster than FlashPCA 1
- Is more accurate than FlashPCA 1
- Uses far less RAM than FlashPCA 1 (in fact, memory usage is bounded)
FlashPCA 2.0alpha has been tested on real and simulated datasets of up
to 1 million individuals genotyped for 100,000 SNPs, and compiles on
both Linux (gcc) and OSX 10.11 (clang).
Pre-compiled binaries are currently not available (you will need to
compile yourself). In addition, FlashPCA 2.0alpha is currently not
supported in R (using the flashpcaR interface).
Advanced users are invited to try out this version and report bugs and
issues either here or at
https://github.com/gabraham/flashpca/issues.
Gad Abraham