julibeg
commented
5 months ago Hi @Kirk3gaard!
Thank you for the feature request. This is on the list of things we would like to include in the workflow, but I cannot give you timelines (or even guarantee that it is going to be included here; it might, for example, be decided to expand the capabilities of wf-16s instead).
If you have a database / reference for your community, you can already use wf-16s to analyse your data (this won't do de novo clustering or similar though).
Regarding the points raised in the linked thread: As noted there, Q28 was achieved and Q30 is within reach. DADA2 needs 10% or more error-free reads in order for the denoising to work. For a 1500 bp gene (e.g. 16S) this would require Q28 or above. This means that full-length 16S ASVs from ONT reads would be possible (which is very exciting).
However, as noted during the last ONT Update at NCM Houston, these improved conditions + basecallers are still under active development. We will revisit the question of DADA2 once they become available.
Is your feature related to a problem?
Most people doing environmental samples do amplicon sequencing for mixed communities so it would be convenient to have a solution for handling this kind of data.
https://x.com/kirk3gaard/status/1750126916152021098?s=20
Describe the solution you'd like
A QIIME/Mothur/USEARCH/DADA2 equivalent for nanopore data.
Describe alternatives you've considered
Some good ideas were mentioned in the replies to this tweet. QIIME/Mothur/USEARCH
Additional context
No response