Taxonomic classification question

[SoilRotifer (Mike Robeson)]

Hi @Vani_Maguire,

@Vani_Maguire

The question is, is it ok to use the 515-806 classifier despite not being the same length extension of my primers (341-805)? or should I use the "full-length" version?

I would recommend using the full-length version if you do not have a set of reference files specifically curated for your amplicon region. Some users on the forum might have have made these files for you, just look around.

Fortunately, we've made a plugin that will allow you to easily prepare your own SILVA classifier. Check out our awesome RESCRIPt plugin. You can follow the tutorial here to make your own classifier based on the 341-F and 805-R primers.

Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt

Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. RESCRIPt RESCRIPt (REference Sequence annotation and CuRatIon Pipeline) is a python package and QIIME 2 plugin for formatting, managing, and manipulating sequence reference databases. This package was designed for compiling, manipulating, and evaluating sequence reference databases from SILVA, NCBI, Greengenes, GTDB, and other sources, and for construc…

Let us know if you run into any issues!

-MIke