IIIandMe: An Algorithm for Chromosome-scale Haplotype Determination Using Genome-wide Variants of Three Haploid Reproductive Cells

Our recent algorithm, Hapi, infers chromosome-scale haplotypes using genomic data of a small number of single gametes. Its advanced version, IIIandMe, is proposed here to achieve comparable phasing accuracy with as few as three gametes, pushing the analysis to its limit. The new method is validated with simulation and a citrus gamete dataset. The rapid advances in genotyping technologies promise a broad application of IIIandMe in disclosing important genetic information.