Annotation and Classifier question

[SoilRotifer (Mike Robeson)]

@ankurnaqib

I did not realize this and its interesting to see that so much good sequences come from these low length reads in the reference database.

Yeah, this is why I tried to make it clear for users to process they way that works best. Ultimately, I really should update that tutorial. For example, I follow the approach as outlined in this figure for my Snakemake pipeline, I also have a Nextflow variant here. I need to clean those up too. Perhaps I should reference these pipelines in the SILVA tutorial?

@ankurnaqib

I have to change the annotation in the taxonomy qza file and the corresponding annotation in the sequences qza file and then re-train the classifier. But is there a way to do that using rescript? Thank you.

Yep, I linked this earlier in the thread, see qiime rescript edit-taxonomy .... You only need to edit the taxonomy file.