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benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution
http://benjjneb.github.io/dada2/
GNU Lesser General Public License v3.0
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What to call a dada2 sequence? #62

Closed jeffkimbrel closed 6 years ago

jeffkimbrel commented 8 years ago

As I explain to other researchers the merits of DADA2, I am always at a loss as to what to call the final sequences from the DADA2 results. I usually just say "OTU", because it is easy to understand, but then quickly clarify they aren't actually OTUs or the results of clustering. I also call them "sequences", but that is too vague of a term. I also sometimes use "taxa", but that won't work universally if people use DADA2 on something other than 16S type data. "Amplicons" also doesn't seem to fit.

Is there any sort of consensus about what to call the individual sequences?

meren commented 7 years ago

They all will all appear as distinct SVs.

Here is my 2 cents on this: How many SVs do originate from a single population is a higher order question, and can't be addressed by general purpose algorithms that aim to partition the marker gene amplicon data into most homogeneous units.

benjjneb commented 6 years ago

On the nomenclature issue, we went with plain-old "sequence variants (SVs)" in this preprint. I believe there are multiple right answers here, and that none of those right answers has "OTU" in it, so we went with the plainest terminology for now.

A final follow-up: After suggestions during review, we changed terminology from SV to ASV, amplicon sequence variant in the final published ISMEJ manuscript: https://www.nature.com/articles/ismej2017119

We have been using ASV since that time, and will continue to use ASV going forward. Thanks for all the comments in this thread, it was a very interesting discussion!

ps: I also want to apologize for accidentally introducing another alternative into the literature. When we changed from SV to ASV in our paper, we didn't change the title "Exact sequence variants should replace operational taxonomic units in marker-gene data analysis", and I suspect we are responsible for "ESV" now popping up in a number of places. Sorry!