OTUs vs ASVs

This forum is designed to help people better understand the theory behind the various commands and options available within mothur
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sapou
Posts: 20
Joined: Wed Jul 02, 2014 5:34 am

OTUs vs ASVs

Post by sapou » Sun Apr 08, 2018 4:32 am

Hi there

I would like to hear your opinion about the ASVs vs OTUs. Do you think that by using amplicon sequence variants we can get a better estimate of the true diversity of a community? Or do you think the technology is still not ready for that? What would be the advantage of continuing using OTUs?

I used the dada2 to get an ASV table from some previously analyzed data (mothur 97%) and the truth is that I got way fewer taxa (ca. 6x less: ca. 3000 OTUs vs 500 ASV). I can see how representative OTUs may inflate the diversity, but isnt that a bit extreme?

Finally, if you think that maybe we can start working with ASVs instead of OTUs, should we expect an option at mothur soon? :D :)

Happy Sunday
P

vingomez
Posts: 24
Joined: Tue Sep 14, 2010 12:02 pm
Location: US EPA

Re: OTUs vs ASVs

Post by vingomez » Tue Apr 10, 2018 9:28 am

Hi sapou,

Here is a comment by Fierer et al., about the subject from last year (see link). A brief summary about Pros and Cons:

http://fiererlab.org/2017/05/02/lumping ... ndon-otus/


I do not want to speak on behalf of Pat, but you can read his comment:

https://www.biorxiv.org/content/early/2017/09/21/192211


Hope it help to begin the discussion.

sapou
Posts: 20
Joined: Wed Jul 02, 2014 5:34 am

Re: OTUs vs ASVs

Post by sapou » Wed Apr 11, 2018 3:22 am

Thanks Vingomez! Hadnt seen that!

I really like Pat's comments, I also believe in the 97% cutoff and I strongly concur that there is a limit to what 250bp of 16S can tell us.
My biggest 'concern' is assessing the diversity of complex bacterial communities, where you can get thousands of OTUs or hundreds of ASVs. Of course I know that most likely we will not find out in this lifetime what is the TRUE diversity there (unless we genome sequence every single strain separately... good luck with that :D ) but I would like to know the one that is closest to the truth. I assume that the reason that dada2 gives fewer taxa (ASVs) is because it has a much more aggressive filtering approach (to remove sequencing errors) but certainly it drops a lot of rare OTUs?
Then again, is there a point of dropping the rare OTUs and keeping only the ones that we are certain about (e.g. the ones above 10 reads perhaps?), in order to create a reduced dataset to compare with?

anyway, its all relative I guess, depending on how we choose to analyze our datasets, in the end its not about the software but about how we interpret the outcome :)

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