Usage of ordinary Nanopore reads

[shelkmike]

The manual of Hifiasm states that Hifiasm can use ultra-long Nanopore reads. Can ordinary Nanopore reads be used by Hifiasm? Since ordinary Nanopore reads are usually longer than HiFi reads, it seems that even ordinary (non-ultralong) Nanopore reads should be beneficial for assembly.

[chhylp123]

Yes, it can. But it would be better to filter out too short ONT reads.

[hrpelg]

Hi, I am interested in feeding hifiasm with hifi reads as with ordinary ONT reads, how can be that done? any specific commands? Cheers

E

[chhylp123]

You can just treat ordinary ONT reads as UL reads.

[Huyuxi08]

Yes, it can. But it would be better to filter out too short ONT reads.

Hi @chhylp123 ! What read length would you recommend filtering out reads below?