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Nextomics / NextPolish2

Repeat-aware polishing genomes assembled using HiFi long reads
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Polishing by HiFi data to draft assembly made of CLR data. #18

Closed Jung19911124 closed 4 months ago

Jung19911124 commented 4 months ago

I am involved in a genome project for a wild animal species with a huge genome (6.5 Gb). We expect the genome to be highly heterozygous, and perhaps over half of it will be repetitive sequences.

Due to budget constraints, we could only obtain x80 coverage of CLR, x20 of Hifi data, and x150 of short-read data. I plan to use CLR to make draft assembly and then use HiFi. Would it be effective to use HiFi data in Nextpolish2 for policing against the draft assembly made with CLR?

Any suggestions would be appreciated.

moold commented 4 months ago

Yes.

Jung19911124 commented 4 months ago

Thank you for your answer.

This animal is very small hence we could not yield enough HMW DNA for CLR and HiFi. CLR and HiFi data were obtained from different individuals.

In this situation (of course, we do not intend to complete phasing perfectly), will the HiFi data from different individual work correctly?

moold commented 4 months ago

Is the sample of short-read data the same as the sample of HiFi?

Jung19911124 commented 4 months ago

No, short read data was from the same indivdual of CLR.

moold commented 4 months ago

So I don't suggest to use NextPolish2 in this case, you can use NextPolish

Jung19911124 commented 4 months ago

Thanks. I will try NextPolish.