Illuminus: A genotype calling algorithm

Illuminus is a program that calls genotype from the Illumina BeadArray platform which does not rely on having prior training data or require computationally intensive procedures. The algorithm can assign genotypes to hybridization data from thousands of individuals simultaneously and pools information across multiple individuals to improve the calling. The method can accommodate variations in hybridization intensities which result in dramatic shifts of the position of the genotype clouds by identifying the optimal coordinates to initialize the algorithm. By incorporating the process of perturbation analysis, we can obtain a quality metric measuring the stability of the assigned genotype calls.


Program Download

A zipped file containing the main codes and example dataset can be downloaded here: illuminus.tar.gz

Please refer to README in the zip file for program instructions.



Please cite the following publication(s) if you are using the program in any publication.

  • Teo YY, Inouye M, Small KS, Gwilliam R, Deloukas P, Kwiatkowski DP and Clark TG. (2007) A genotype calling algorithm for the Illumina BeadArray platform. Bioinformatics (Oxford, England), 23(20), 2741-2746