For genome with extremely rich simple repeat sequences

[YouxinZhao]

My assembled genome species has a genome size of 2.6 Gb with extremely rich simple repeat sequences. I assembled it using 21x Hifi, trio data, and 15x ONT (>40k) data, resulting in genome sizes of 1.2 Gb and 1 Gb, with N50s of 170K and 166K, respectively. When using only HIFI data, Hifiasm yielded a genome size of 1 Gb, with a contig N50 of 54 kb. However, I used NExtdenove to assemble only the 15x ONT data, and obtained a genome size of 1.8 Gb, with a contig N50 of 1.5 Mb, which is significantly higher than the assembly results obtained from Hifiasm. This is just an early assessment, we are increasing the sequencing data. And I am considering adjusting the sequencing strategy, as it seems that the 15K Hifi data is unable to span through the simple repeat region. I am wondering if Hifiasm is capable of handling the task of genome assembly of this species. Do you have any suggestions?