Benjamin Callahan

> Was that referring to PacBioErrfun or another function? A different function. Pacbio has changed the way Hifi quality scores are determined, and `PacBioErrfun` is no longer recommended for Pacbio...

Yes I think so. We'll have more to say later though as we are just working through our first full Revio dataset. It does seem to be a repeated observation...

> Do you think the binned quality scores model is matured enough for Revio Kinnex data? The only benchmark with truth I have is the MSA1003, and that worked even...

My first thought is that this might be an interaction between the reference database and the naive Bayesian classifier method implemented by `assignTaxonomy`. Do you have the outgroups needed for...

Hm... have you tried `assignTaxonomy(..., tryRC=TRUE)`? If some of your ASVs are in the opposite orientation to the database, you can get weird assignments. But `tryRC=TRUE` will also test the...

Note to self: Multiple reports of issues with `assignTaxonomy` and the UNITE db have been cropping up recently. Something to monitor going forward.

Could you clarify which command exacly is throwing this error? I'm not clear from your original post whether it is `dada` on the reverse reads, or `mergePairs` subsequently. Whichever command...

The appropriate files to use with `assignTaxonomy` are the General Fasta releases (with 10s of thousands - 200k sequences), not the UNITE+INSD relsease (with 2-8M sequences).

1. What you are doing is fine. You really only need the `maxEE` filter (it is doing a slightly more sophisticated version of average quality filtering). 2. I don't recommend...

Thanks @ep142 ! I've added these as highlighted contributed references on our taxonomic reference data page https://benjjneb.github.io/dada2/training.html I also really appreciate your excellent sanity test scripts.