Haplotype-resolved genome assemblies of the Friesian horse and the Dutch Warmblood horse using the trio-binning method
We performed nanopore sequencing (R10.4, Q20+) of an F1 cross between a Dutch Warmblood horse and a Friesian horse to create two breed-specific reference assemblies using trio binning. Triocanu was used to bin the nanopore reads (80X) of the F1 cross using the short reads (50X) of the parents. Then, we used Flye and RagTag software to create and scaffold both assemblies. Scaffolded assemblies were validated with breed-specific linkage maps based on 70K genotypes. This resulted in two high-quality, haplotype-resolved reference assemblies (contig N50 was 35Mb and 37Mb and single copy gene completeness was 99.2% and 99.3%, for the Dutch Warmblood horse and Friesian horse, respectively).