C-YONG

Based on my understanding, this option will genotype all snarls, including those nested within other snarls (similar to the behavior of the deconstruct -a command). Nested snarls are variations that...



Thank you for your answer！ Regarding the haploid chromosome number (n): Yes, my species has 2n = 40, so the haploid chromosome number (n) is 20. Regarding the similarity in...

Thank you for your suggestion. With the new parameters, I successfully located the 20 chromosomes. However, I noticed that some chromosomes show terminal signal issues, and I suspect there might...

I understand what you mean. I apologize for asking again, but is it better to combine the two haplotypes and perform the scaffolding together? This way, we can identify potential...

Hello, after merging the haplotypes and performing scaffolding, I found that two chromosomes exhibited haplotype collapse. Since my goal is to assemble a haplotype-resolved T2T genome, I encountered issues during...

Alternatively, can I directly use the sequence from the homologous contig to fill the gap? Would this approach be feasible?

I used HiFi data to calculate the coverage at the collapsed region. How can I precisely locate the start position of this collapsed region? The approximate location can be determined...

Thank you for your response. We attempted to align p_ctg.fa to p_utg.fa using minimap2 `minimap2 -x asm5 `. We found that two unitigs aligned to the same contig, but the...