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nanoporetech / medaka

Sequence correction provided by ONT Research
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polish with ONT reads from different model #435

Closed cjchen5 closed 10 months ago

cjchen5 commented 1 year ago

Hi,

My draft genome is assembled with ONT reads generated from Min and Prom. I would like to use all ONT reads for polish but as ONT reads contain different models, I can't do this.

Any suggestion for how to deal with this situation? Can the model be set for each ONT reads file?

Thanks!

cjw85 commented 1 year ago

I cannot provide any clear advice here as it is not something we typically do. All I can suggest is trying a few experiments using each medaka model with the different facets of your data and all your data combined.

cjchen5 commented 5 months ago

Hi, Is there any update on this question now? I have two fq files with models r1041_e82_400bps_hac and r1041_e82_400bps_sup. Is that possible to select different models for different fq? Or do I have to generate it with the same basecaling model and then medaka?

In addition, if I have to generate it with the same basecaling model, should I restart assembly or I only need to new generate fasta reads for polishing? Thanks!

cjw85 commented 5 months ago

All the medaka models are intended for use with a single basecalling model, with assemblies generated from from the same reads.

cjchen5 commented 5 months ago

All the medaka models are intended for use with a single basecalling model, with assemblies generated from from the same reads.

Thanks for your quick response! Just double checking, the suggestion is to restart the assembling with reads used with a single basecalling model?

cjw85 commented 5 months ago

Correct