Recommendations for using long-read datasets

[Serka-M]

Thank you for developing this awesome tool.

I was wondering if singlem (specifically the microbial fraction module) would work adequately on Nanopore/PacBio long-read datasets (metagenomic reads and assemblies)?

Or are there any special settings that would optimize for long, slightly erroneous reads?

Best,
Mantas

[wwood]

Hi Mantas,

Thanks for the kind words.

We have a plan for incorporating nanopore reads (there's an additional complication that if multiple genes are encoded by singlem will not work well), but aren't there. I hope I can say something more soon.

microbial_fraction is especially prone to that problem, I would hazard a guess.