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Nextomics / NextPolish2

Repeat-aware polishing genomes assembled using HiFi long reads
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The number of gaps will decrease after running nextpolish2 #23

Closed zhoudreames closed 2 months ago

zhoudreames commented 2 months ago

My raw genome contains 45 gaps, the number of gaps decrease to 41 after run the code "nextPolish2 -r -t 100 HiFi.bam ref.fa Illumina.k21.yak Illumina.k31.yak >ref.polising_1.fa", while then umber of gaps decrease to 35 when I add the parameter -r . I don't know if this is a normal phenomenon, as I noticed that the usage method did not mention the function of filling gaps for nextpolish2

zhoudreames commented 2 months ago

@kaichop @moold @WonderOmics @dongyawu i am so sorry to disturb you, would you help me ? thanks

moold commented 2 months ago

Please don't @ people, because this is a free Q&A, especially people who are not related to this repository. If I am free, I will answer the question as soon as possible. If I don't have time, please just wait, I will reply later. To reiterate, this is a free Q&A.

nextPolish2 does not contain gap filling steps, but if some gaps can be spaned by hifi reads, these gaps may be closed in some extreme cases. You can map hifi reads to the polished genome and use IGV to check the reliability of these gap filling regions.