Hapi - Chromosome-length haplotype inference using genotypic data of single gamete cells

Please cite the following publication:

Li, R., Qu, H., Chen, J. et al. (2020). Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes. Molecular Biology and Evolution

Introduction

Hapi is a novel easy-to-use and high-efficient algorithm that only requires 3 to 5 gametes to reconstruct accurate and high-resolution haplotypes of an individual. The gamete genotype data may be generated from various platforms including genotyping arrays and sequencing even with low-coverage. Hapi simply takes genotype data of known hetSNPs in single gamete cells as input and report the high-resolution haplotypes as well as the confidence level of each phased hetSNPs. The package also includes a module allowing downstream analyses and visualization of identified crossovers in the gametes.

Manual and R script

The comprehensive manual of Hapi is available here: Hapi Manual.
R code of the workflow is available here: Hapi Workflow

Installation

install.packages('Hapi')