Concatenamer Removal Before EMU Classification with Nanopore 16S rRNA Data

[ctmlab4]

Hi everyone,

I'm new to using EMU with 16S rRNA data generated via Nanopore sequencing, thank you for developing and sharing such a great tool!

I have a question regarding preprocessing: is it necessary (or recommended) to remove concatamers from the raw reads before running EMU classification? I'm wondering if this step could improve the accuracy or quality of the taxonomic assignments.

Has anyone had experience with this or could share their workflow?

Thanks so much.

Best,
C.

[kdcurry]

Our tests for the manuscript showed better results without concatamer filtering, but I imagine this could really vary. I'd recommend running a quick test to get a sense of how prevalent concatemers are in your sample. I believe there are several softwares for this, or perhaps you could get a sense by just evaluating your read lengths.

[ctmlab4]

Hi @kdcurry,

I just checked the quality of my sequences, which I basecalled using simplex SUP with Dorado, and I found duplicated sequences corresponding to the conserved regions of the 16S rRNA. Does this mean that I did not account for a high amount of concatamers right?

Thank you so much!

[kdcurry]

I think it depends on what you mean by "duplicated". Sequences can be identical without being concatamer.