I have a reference genome with multiple N gaps. I also did a de novo assembly with hifiasm which gave me good results.
Do you know if there is a tool or method to fill the gaps from the reference genome with my assembly?
Is the reference exactly the same species/strain? If they aren't basically identical this is probably not a very good idea if you plan to do any 'proper' analysis based on it.
It is exactly the same species.
Agreed. Unless they are the same strain, this should probably be avoided.
Can you just use your new denovo assembly for downstream analysis?
The aim would be to know if I could fill the N gaps with my denovo assembly. Obviously, my denovo assemby is sufficient for downstream analysis.
maybe by cheating around with cobbler (https://github.com/bcgsc/RAILS)?
I didn't know this tool, I will try. I also used https://github.com/malonge/RagTag
Login before adding your answer.
Use of this site constitutes acceptance of our User Agreement and Privacy