Most metabarcoding pipelines such as dada2 do not include singletons in their analyses pipline. In some situations, it is, however, interesting to include singletons at least for alpha diversity calculations (the singletons were obtained by q2 vesearch cluster-features-de-novo). This paper (Estimating and comparing microbial diversity in the presence of sequencing errors [PeerJ]) descibed how to handlle spurious singletons in alpha statistics.
I looked at the q2 diversity alpha parameters and tried to open the link given in the help menu (https://data.qiime2.org/a_diversity_metrics), but it seems that this link is no longer existing.
Is there an updates link available?
Does anybody know if one of the available parameters already correspond to the procedures mentioned in the paper mentioned above?
Hi @arwqiime, This document has references for the different available metrics (for both alpha and beta diversity). Does that get you the information that you're looking for?
Related, it's cool to see Dr. Anne Choa still working on alpha diversity. Her 1984 Choa1 method appears to not be a good fit for singleton-free ASV methods like DADA2:
(Thank you @timanix for recommending this paper to me!)
It appears that this problem can be addressed by using DADA2 'pooled'
It looks like Choa has been aware of this problem for awhile, so thank you for brining that paper to my attention! I'll have to look into Hill numbers.