Method to fill N gaps with de novo assembly

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2.5 years ago

pablo ▴ 310

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 • 1.2k views

ADD COMMENT • link 2.5 years ago by pablo ▴ 310

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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.

ADD REPLY • link 2.5 years ago by Joe 21k

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It is exactly the same species.

ADD REPLY • link 2.5 years ago by pablo ▴ 310

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

ADD REPLY • link 2.5 years ago by samuel.a.odonnell ▴ 580

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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.

ADD REPLY • link 2.5 years ago by pablo ▴ 310

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

ADD REPLY • link 2.5 years ago by Juke34 8.9k

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

ADD REPLY • link 2.5 years ago by pablo ▴ 310

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