September 25, 2013

sNMF for fast estimation of admixture coefficients

This seems quite a useful improvement in performance, especially for those who are CPU-limited. The software is available here.

UPDATE (Feb 6): This paper has now been published in Genetics.

arXiv:1309.6208 [q-bio.PE]

Fast Inference of Admixture Coefficients Using Sparse Non-negative Matrix Factorization Algorithms

Eric Frichot et al.

Inference of individual admixture coefficients, which is important for population genetic and association studies, is commonly performed using compute-intensive likelihood algorithms. With the availability of large population genomic data sets, fast versions of likelihood algorithms have attracted considerable attention. Reducing the computational burden of estimation algorithms remains, however, a major challenge. Here, we present a fast and efficient method for estimating individual admixture coefficients based on sparse non-negative matrix factorization algorithms. We implemented our method in the computer program sNMF, and applied it to human and plant genomic data sets. The performances of sNMF were then compared to the likelihood algorithm implemented in the computer program ADMIXTURE. Without loss of accuracy, sNMF computed estimates of admixture coefficients within run-times approximately 10 to 30 times faster than those of ADMIXTURE.


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