Hi,

I am new to genome assemblies and I am now trying to manually curate my assembly to chromosome-level assembly. I have a scaffolded assembly with about ~300 scaffolds, and would like to join and break some scaffolds and arrange it to 23 chromosomes. What can I do to do this?

I have aligned my scaffolds to a reference genome to see which scaffolds are in which chromosomes however I do not have an idea how I can arrange my scaffold, assign them to a chromosome number and combine them, and make it into chromosome-level assembly. Can you please give me some idea how to do it?

Thanks!