Clarification for OTU versus ASV in rep-seqs and .biom tables

[microbiomeAnalyst]

I wanted to verify that the sequences represented in rep-seqs.qzv (version 2019.1) are amplicon sequence variants (ASV’s). So each of the 760 distinct feature IDs would represent a unique sequence variant? I want to ensure these are not in any way OTUs, although I think of sequence variants as “100% OTUs.”

Also, when I review the .biom table (converted to a .tsv) the column label is #OTU ID . Is this “OTU#” interchangable with ASV?

Am I correct that if dada2 for version 2019.1 is run for denoise, both the .biom table and the rep-seqs.qzv should reflect sequence variants and not OTUs? Is this simply semantics for this version?

Thank you!

[Nicholas_Bokulich]

@microbiomeAnalyst

Also, when I review the .biom table (converted to a .tsv) the column label is #OTU ID . Is this “OTU#” interchangable with ASV?

this is a biom-format-specific convention, not QIIME 2 (features are usually labeled "feature-id" or similar in QIIME 2 to reflect the ambiguity, but this is plugin specific).

@microbiomeAnalyst

Am I correct that if dada2 for version 2019.1 is run for denoise, both the .biom table and the rep-seqs.qzv should reflect sequence variants and not OTUs? Is this simply semantics for this version?

Correct. Some naming and format conventions are slow to change.

You definitely have ASVs if you used dada2, even if the table is labeled "OTU ID"