Question: Faster version of STRUCTURE
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gravatar for a_elakhdar
22 months ago by
a_elakhdar0
a_elakhdar0 wrote:

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?

snp structure • 476 views
ADD COMMENTlink modified 22 months ago by Philipp Bayer6.4k • written 22 months ago by a_elakhdar0
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gravatar for Philipp Bayer
22 months ago by
Philipp Bayer6.4k
Australia/Perth/UWA
Philipp Bayer6.4k wrote:

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)

ADD COMMENTlink written 22 months ago by Philipp Bayer6.4k
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