which asm.fa should be used in nextpolish2? the contig.fa or genome.fa

Nextomics / NextPolish2

Repeat-aware polishing genomes assembled using HiFi long reads

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which asm.fa should be used in nextpolish2? the contig.fa or genome.fa #15

Closed QianghuiZhu closed 7 months ago

QianghuiZhu commented 7 months ago

Hi! NextPolish2 is a great software for correcting errors. I have poor knowledges about assembly. And I want to know which asm.fa should be used in nextpolish2? I run hifiasm and got contig.fa. And after running juicer and 3d-dna, I got the genome.fa. May I use genome.fa directly in nextpolish2? Or maybe should I use contig.fa with nextpolish2 first, then run juicer and 3d-dna, and fix the genome.fa with nextpolish2 again? Thanks!

moold commented 7 months ago

genome.fa is OK.

QianghuiZhu commented 7 months ago

OK. Thanks for this!