Does anyone know how effective nf-core taxprofiler would be if you’re trying to identify the identity of DNA from a monoculture, or DNA from mostly pure monoculture that could have a little bit of DNA from other organisms? Or does this pipeline explicitly need to be used for metagenomic samples?

No, it's generic 🙂

You could set your expected culture species as the host genome and try your luck with the rest of the reads.

I’m more interested in host strains. Our group has a culture collection. It has just never been passaged on antibiotics so it might be a bit dirty. But we would like to know the phylogenetics of all our strains. I was wondering if this pipeline would be appropriate

Ah, I thought you expected contamination. No, I don't think tax profiler is appropriate for your problem.

Why not?

Your strains might be down to SNPs and the reference databases used by taxprofiler are much more crude. They are typically not made to resolve below species rank.

Okay perfect that’s what I wanted to know.

Not my forte but try http://segatalab.cibio.unitn.it/tools/strainphlan/ perhaps?

Thank you

@James Fellows Yates can you help with that? 😛

Should have a n email invite

Thank you!!