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Nextomics / NextPolish

Fast and accurately polish the genome generated by long reads.
GNU General Public License v3.0
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gap filling effects? #98

Closed EugeneKim76 closed 2 years ago

EugeneKim76 commented 2 years ago

NextPolish What version of NextPolish are you using? 1.3.1 You can use the command nextPolish -v to get it.

Dear all, I polished my assembly using long reads and nextpolish.
There are 7 small gaps (each length is 13Ns) in my assembly. I checked the manual, and identified that it is recommended to split the assemblies at the gaps, then polish it using nextpolish. However, I found the polishing step resulted in filling all the gaps. How can I understand the result? I'm so confused since it is considered that some researchers are using nextpolish as a gap filling tool. There are some examples on googlescholar. (search by keywords : nextpolish, gap filling). Best,

moold commented 2 years ago

For gaps that some reads can span, nextPolish can use these spanned reads to close those gaps. For other gaps, nextPolish may cause undefined behavior.

EugeneKim76 commented 2 years ago

Dear moold, Thanks for your quickly reply Best,