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schmeing / gapless

Gapless provides combined scaffolding, gap-closing and assembly correction with long reads
MIT License
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Can I use only GAPLESS to fill the gap? #8

Open XXH123a opened 1 year ago

XXH123a commented 1 year ago

Dear Developer Excuse me, I already have a genome at the chromosome level, so I just want to try filling gap with GAPLESS. Do you think it's okay?

schmeing commented 1 year ago

In the gapless.py there is a parameter org_scaffold_trust that is by default set to "basic". If you set it to "blind", it should only fill gaps. I did not pull this parameter through to the program parameter level, yet. I will do this, but currently I am changing flats, so it will likely not happen before the end of the month. Thus, if you want it fast you have to change it directly in the python file.

XXH123a commented 1 year ago

Thank you for your enthusiastic guidance. I will immediately give it a try and compare it with LR_ Gapcloser, TGS-gapcloser results.

xizhesun commented 1 year ago

@XXH123a Hi, could you share the compare result?

xiekunwhy commented 10 months ago

also just want to use gapless to fill gap only.