This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Method to fill N gaps with de novo assembly

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

assembly
• 2,063 views • link
written by pablo pablo

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.

• 0 views • link
written by Joe Joe

It is exactly the same species.

• 0 views • link
written by pablo pablo

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

• 0 views • link
written by samuel.a.odonnell samuel.a.odonnell

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.

• 0 views • link
written by pablo pablo

0 answers

No answers yet.

Log in to answer this question.

More posts like this