Faster version of STRUCTURE

Question

[a_elakhdar]

I am attempting to run my SNP dataset in STRUCTURE, at 10K burnin and 10K MCMC reps. I have 7864 loci and 84 individuals. so I ran for K=1 to K=20, at 5 iterations. Now, I am waiting days on my laptop for STRUCTURE to run! I saw on another post that there is a faster version of STRUCTURE in the works - do you have any recommendations on how to speed up the process?

Answer 1

[Philipp Bayer]

fastSTRUCTURE has been released 3 years ago: https://rajanil.github.io/fastStructure/

Paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4063916/

Takes binary PLINk files (bed/bim/fam) as input, I've had good success with it (definitely much faster than STRUCTURE but I have no numbers right now)