Perfect! Just gives more control over your reference database.
I have a small (!) concern regarding edit taxonomy.
I trained Silva database for V3-V4 region using Rescript and observed many misannotations as you give example above "edit taxonomy" part. I am a bit scared to manually edit each single of them every single time I did a taxonomic assignment. I am working on the marine environment. Do you think preparing a single search and replacement metadata file can be used in different projects or every time I got new data I should prepare a new metadata file to edit taxonomy? I just could not foresee if taxonomic assignment mistakes will be approximately the same or not. If you catch approximately more than 500 ASVs in each project, then editing might be painful each time.
I realized that I never explicitly stated the goal of edit-taxonomy. So, I added the following statement to the tutorial:
Typical use cases:
Edit the taxonomy prior to generating a taxonomic classifier.
Make taxonomy more "friendly" for plotting figures
Relabel non-official / un-accepted taxonomic labels, which are likely to cause confusion.
Truncate taxonomic names (e.g. based on a regular expression) so that the full lineage is not displayed in something like a heatmap.
Or any other reasons we've not listed here.
If modifying the taxonomy for the first use case, there should be no need to edit the taxonomy each time you analyze your data. But it'd be a good idea to maintain / update your metadata file as you encounter additional mis-annotations. Then just use that whenever to make a classifier.
