Taxonomy Classification Best Practices?

[SoilRotifer (Mike Robeson)]

Hi @ashamarie,

I might need some additional details to help... Note, most are just sanity-check questions.

1. What amplicon region are you actually sequencing and trying to classify?
   • Are you actually sequencing with the V4 region with the 515F 806R primers?
2. What is "self-trained"?
   • That is, what database was the reference sequence and taxonomy compiled from?
     • SILVA
     • GreenGenes
     • GenBank
     • GTDB
     • ... ?

In general, you'll likely see more diverse "hits" with SILVA compared to GreenGenes, as it is a much larger reference database.

@ashamarie

You can see the classification resolution varied dramatically, and we are unsure of whether using a self-trained classifier is actually the most appropriate method.

We have just the tool for you, to help answer such questions. Check out RESCRIPt! Here is the current tl;dr install.

-Thanks!
-Mike