Method to fill N gaps with de novo assembly

Question

[pablo]

Hello,

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?

Regards

[Joe]

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.

[pablo]

It is exactly the same species.

[samuel.a.odonnell]

Agreed. Unless they are the same strain, this should probably be avoided. Can you just use your new denovo assembly for downstream analysis?

[pablo]

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.

[Juke34]

maybe by cheating around with cobbler (https://github.com/bcgsc/RAILS)?

[pablo]

I didn't know this tool, I will try. I also used https://github.com/malonge/RagTag