Hi, I have generated a genome assembly using the latest version of verkko. The outputs was asssembly.haplotype1.fasta, assembly.haplotype2.fasta as well as assembly.unassigned.fasta. I extracted the unassigned contigs found on the assembly.unassigned.fasta and ran seqtk -l 10 to search for telomeric repeats in these extracted unassigned contigs.

The telomeric repeats were present and are in the p-arms of some of the acrocentric chromosomes. My question is how do I then patch these p arms to their corresponding chromosomes, so that I have a full chromosome with both the p and q arms? I used HiFi + ONT-UL and OmniC data