Abstract Knowledge of chromosome-length haplotypes will not only advance our understanding of the relationship between DNA and phenotypes, but also promote a variety of genetic applications. Here we present Hapi , an innovative method for chromosomal haplotype inference using only 3 to 5 gametes. Hapi outperformed all existing haploid-based phasing methods in terms of accuracy, reliability, and cost efficiency in both simulated and real gamete datasets. This highly cost-effective phasing method will make large-scale haplotype studies feasible to facilitate human disease studies and plant/animal breeding. In addition, Hapi can detect meiotic crossovers in gametes, which has promise in the diagnosis of abnormal recombination activity in human reproductive cells.

Inference of Chromosome-length Haplotypes using Genomic Data of Three to Five Single Gametes