Taxonomy diversity

[Nicholas_Bokulich]

@Will_Ericksen

what do you mean by 'no more maintained'?

The developers are no longer making new releases and their website is down (at least right now! and the past few times I tried)

@Will_Ericksen

Do you mean that if I use the latest version of qiime2, I can no longer use the RDP database for taxonomy classification?

No, you can absolutely use the RDP database with QIIME 2 if you can find a copy of the database (see below).

@Will_Ericksen

Or can I still use it, but you no longer perform updates on the database?

Half correct. You can still use it, but RDP will no longer make any new releases (and have not for a few years). The significance being that the taxonomy may go out of date, and newer species and sequences will be missing.

The QIIME 2 developers have nothing to do with RDP, so it's not the QIIME 2 developers who are no longer updating RDP.

see this post for some related info:

Best sequence database for classifying 16s v4 sequences of human stool samples

I agree with @jwdebelius, it depends on your questions, and the resolution by which you analyze your data. I also prefer to analyze via ASVs, as they will not change... but the taxonomy assigned to them might change at a later date given the ever changing world of microbial taxonomy. The taxonomy will also vary between databases depending on the taxonomic schema, and nomenclatural rules they decided to follow. Some other thoughts ... I became aware that RDP is no longer funded, and is likely …

We do however have a tutorial for importing and using the RDP database with QIIME 2 if you want to use this database (I think the data are still available in a few places on the internet even if their website is currently down):

Importing sequence data with lower-case nucleotide characters. Constructing an RDP classifier as an example.

With the recent qiime2-2022.11 release, we can now import DNA and RNA sequence files that contain lower-case sequence characters. Upon import, these nucleotide bases will be converted to the standard upper-case IUPAC format, using the new MixedCase* import formats. A few examples of which are listed below: MixedCaseAlignedDNAFASTAFormat MixedCaseAlignedRNAFASTAFormat MixedCaseDNAFASTAFormat MixedCaseRNAFASTAFormat Example use case: The Ribosomal Database Project (RDP) We'll import a recent v…