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mikolmogorov / Flye

De novo assembler for single molecule sequencing reads using repeat graphs
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Q: input settings for HERRO-corrected ONT reads #738

Open aistBMRG opened 1 week ago

aistBMRG commented 1 week ago

Hi,

Small question -- it was touched upon in another thread but I could not find exactly what I was looking for. For HERRO-corrected ONT reads, would it be possible to suggest the best type of input format to specify? I guess the quality approaches that of PacBio HiFi, but the input should be nano-hq, is my understanding correct?

Thank you for your time and amazing assembler.

Best,

Dieter

mikolmogorov commented 2 days ago

Hi Dieter,

Sorry for my late response! We have not tested HERRO-corrected input extensively, but I think --nano-hq should work. I also recommend setting the expected read error rate to a lower value using --read-error

aistBMRG commented 2 days ago

Thank you very much for clarifying. I understand, and will give it a try - I will let you know if any unexpected results show up.

Dieter