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Nextomics / NextPolish2

Repeat-aware polishing genomes assembled using HiFi long reads
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Correction of haplotypes #11

Closed monian1113 closed 1 year ago

monian1113 commented 1 year ago

If I am using haplotype assembly with hifiasm via hic data instead of trio data, will NextPolish2 be able to do haplotype aware error correction, and what should I do in this case?

moold commented 1 year ago

Yes, just follow the usage docs, no extra steps.

monian1113 commented 1 year ago

Yes, just follow the usage docs, no extra steps.

Should I combine hap1 and hap2 for reads mappimg, or first isolate the reads that match hap1 or hap2 separately and then correct each haplotype separately?

moold commented 1 year ago

I suggest mapping and correcting each haplotype separately. BTW you can also try both strategies to see which one is better.