Haplotype assembly without parental sequencing: Genotype-based trio-binning (GT-Trio)

Trio-binning is a robust method for haplotype-resolved assembly, providing the most accurate representation of diploid genomes including complex and haplotype-specific variation. Conventional trio-binning methods depend on parental short-read sequences to differentiate offspring reads originating from the maternal and paternal haplotypes. Here, we present a genotype-based trio-binning pipeline (GT-Trio) which reconstructs parent sequences from phased parental genotypes and uses this as an alternative source of parental information for haplotype assembly. The GT-Trio pipeline was applied to assemble the maternal and paternal haplotypes of three Norwegian Red (NR) cattle individuals, using phased parental genotypes imputed from array to sequence as input. Haplotypes assembled with GT-Trio using all sequence variants as parental input demonstrated assembly quality and phasing accuracy comparable to that achieved with conventional trio-binning. Using lower density subsets of array SNPs led to a slight reduction in accuracy of haplotype separation, accompanied by an increase in size, contiguity and completeness, suggesting a trade-off between assembly quality and phasing accuracy associated with the density of parental genotypes provided as input to the pipeline. Overall, GT-Trio provides a scalable framework for haplotype assembly without parental sequencing and will be applicable in livestock species where genotyping and imputation is performed routinely. The GT-Trio pipeline is available at https://github.com/theahettasch/GT-Trio.