Unbalanced homeologous exchanges are collapsed

[zhangrengang]

My allotetraploid genome has a few homeologous regions that are derived from the same diploid ancestral species (unbalanced homeologous exchanges). In the final primary assemblies (p_ctg, hap1.p_ctg and hap2.p_ctg), some of these regions are collapsed. How can I improve the completeness of these regions?

[lh3]

Whether this is resolvable highly depends on the length and sequence divergence of these regions. You have to analyze case by case.