Adding ONT read support for ampliseq

[ShareiFae]

Description of feature

Would it be possible to add support for Oxford Nanopore Technology reads? I've found two projects (the second integrating the first) that might allow a quick implementation.

https://github.com/treangenlab/emu
https://github.com/genomic-medicine-sweden/gms_16S

[d4straub]

Hi @ShareiFae ,
emu seems indeed interesting, its also available as container https://bioconda.github.io/recipes/emu/README.html.
However, if I understood correctly, it compares sequences to a database and makes count tables from that. It is not a reference-free (de-novo) representative sequence (OTU/ASV/whatever) calculation like DADA2 or Deblur. Therefore I have the impression the tool is misplaced in this pipeline. Let me know if you have a different opinion.

[ShareiFae]

A shame, the downstream analysis and the report of this pipeline is really really good and I would like it to have it with nanopore data even it they cannot be done exactly the same way.

With EMU, as demonstrated by this other pipeline, you can create a phyloseq object that functions as Pseudo OTU tables:
https://github.com/josephpetrone/RESCUE/blob/master/detailed_steps.md#rstudio-and-phyloseq-handoff
https://github.com/josephpetrone/RESCUE

I've also found a pipeline that utilizes Quiime:
https://github.com/MaestSi/MetONTIIME