DADA2 with SILVA 99% OTU classifier

[Nicholas_Bokulich]

Just to add to @timanix 's great answers

@Coldgrad

It is my understanding, however, that DADA2 produces ASV-level sequencing data, whereas we're classifying using an OTU-based classifier.

It is possible to make a dereplicated (but not clustered) reference database with the plugin RESCRIPt. This was actually one motivation for RESCRIPt: to make it easier to build databases, but also to build and test dereplicated (rather than clustered) databases.

In practice the difference between a 100% dereplicated and 99% clustered database is not all that big. The clustered database is rather more efficient, but it is possible to make a dereplicated database, see the instructions for using RESCRIPt here (for SILVA and NCBI databases):

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…

Using RESCRIPt to compile sequence databases and taxonomy classifiers from NCBI Genbank

This tutorial will describe how to create custom reference databases from NCBI Genbank using RESCRIPt. Read more about RESCRIPt here: Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt - #7 If using NCBI Genbank data, please be aware of the NCBI disclaimer and copyright notice. Citation: If you use RESCRIPt or any RESCRIPt-processed data in your research, please cite the following pre-print: Michael S Robeson II, Devon R O'Rourke, Benj…