Chris Fields

> Are there also separate taxonomy files for the new databases or I have to extract it from the fasta files? > > I'm finding some missing taxonomies, e.g. in...

Hi all, we're almost at the 10 year mark for this pull request (which I think we can safely close). @prvst did you have any additional comments on it?

Thx @benjjneb , I can have a look to see if I can sus it out.

@dawsonfairbanks do you know if the sequences are Q20 (99% base accuracy) or Q30 (99.9% base accuracy)? Looking at the error plot it looks more like 99%, but worth checking....

Just to add: we have the very same issue with another project, which is essentially bleed over from barcode hopping (these were from COX1 amplicons). The only option we had...

It does appear there are issues with `learnErrors`, at least when using our workflow. We run this script: ```{r} filts

It looks like the issue above was a workflow problem (the task timed out). However we are seeing increased loss of sequence data compared to past runs, and there are...

We just tried a run using the alternative function for error estimation provided by @jonalim and tested by @hhollandmoritz here: https://github.com/benjjneb/dada2/issues/1307#issuecomment-957680971 (option 4). This seems to help, though the data...

This is an updated plot with `nbases=1e10`  I should mention that the PacBio workflow steps for Kinnex still appear to use the original `PacBioErrFunc`. We are downloading their Zymo...

Error profiles for the mock community samples from here: https://downloads.pacbcloud.com/public/dataset/Kinnex-16S/DATA-ZymoATCCMix-32plex-Revio/2-Demux/fastq_files/ ## The original PacBio model, `PacBioErrfun` code: ``` errs