In our initial experiments, we’ve found that low heterozygosity allotetraploids are better treated resolving to the level of subgenome rather than haplotype. Attempting to resolve low heterozygosity polyploids will likely result in low completeness of the haplotype-resolved assemblies. Higher heterozygosity allotetraploids contain sufficient variation to enable resolution at the haplotype level. The workflow is shown in Figure 1.
Figure 1. High-heterozygosity workflow.