Abstract
Haplotype-resolved genome assemblies remain a challenge in practice. Here, we provide a step-by-step guide on gamete binning, a method to generate haplotype-resolved genome assemblies for diploid species. The protocol starts by phasing heterozygous variants to individual haplotypes of specific chromosomes using the genome information of individual haploid gametes of the focal individual. Using phased variants, the whole-genome sequencing reads from the diploid genome can be genotyped and assigned into groups, which represent the individual haplotypes of each of the chromosomes. Finally, haplotype-specific chromosomes can be assembled independently using standard assembly tools. First applications of gamete binning revealed a haplotyping accuracy over 99%, which outperformed sequence-only or Hi-C-based haplotype-resolved genome assemblies.Availability: github.com/schneebergerlab/GameteBinning_prac .
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