archaea , bacteria and the SILA database

[Mantella86 (Martyn)]

Hi all. Just a quick question I hope someone can hekp with. Can i use SILVA 138 database for the V3 and V4 region of bacterial 16 S rRNA gene with primers Bakt_341F and Bakt_805R and the V6-V8 region of the archeal 16S rRNA with the primers A956F and A1401R.

Or does it require something different?

Best wishes

[SoilRotifer (Mike Robeson)]

Hi @Mantella86,

Yep! You can either use the full-length SILVA SSU sequence database available on the Data resources page, or you can curate your own SILVA-based classifier with RESCRIPt for your target region of interest:

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…