How to generate an ASV table from DADA2 output?

[Nicholas_Bokulich]

@Clara

I have generated my OTU table in the taxonomy analysis step and recently get to know very little about ASV (if someone can explain it to me in a simple words that will be much appreciated).

You can think of ASVs as being 100% OTUs that have gone through some sort of denoising process. So instead of being operational taxonomic units clustered as some % threshold as a crude method for reducing noise by collapsing into clusters, they are amplicon sequence variants that recover true signal from the sample. I recommend this paper for a better idea of the transition from ASVs to OTUs.

@Clara

Since I am using DADA2 in QIIME2, I wonder I have already generated my ASV outputs in terms of rep-seqs-dada2.qza, stats-dada2.qza and table-dada2.qza, am I right?

Correct!

@Clara

how can I “use” this ASV table?

Same exact way as an OTU table. Both ASV and OTU tables are types of "feature tables" (feature being a generic term since this type of observation matrix can really contain all sorts of information). See the QIIME 2 tutorials for many examples of what one can do with a feature table.

@Clara

Or how can I transform them into a readable table form? Is it by converting them from a .qza format into a .biom file?

Correct

@Clara

Can they be treated just like an OTU table?

Yes!

Good luck!