classifier for fungi data analysis

[SoilRotifer (Mike Robeson)]

Hi @AnaBanana,

I am unaware of an existing reference set or classifier for this marker gene. Perhaps someone else in the forum will reply here.

However, we do have this nice plugin called RESCRIPt that enables you to make your own reference set . I think this tutorial would be the most beneficial:

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: https://forum.qiime2.org/t/processing-filtering-and-evaluating-reference-sequence-data-with-rescript/15494/7 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, Benjami…

Some other general examples can be found on the forum, e.g.:

Create NCBI database for identifcation with ITS region

I forgot to mention you can try setting up a more generic queries... like: Streptophyta: --p-query "txid35493[ORGN] AND (ITS OR Internal Transcribed Spacer) NOT environmental sample[Title] NOT environmental samples[Title] NOT environmental[Title] NOT uncultured[Title] NOT unclassified[Title] NOT unidentified[Title] NOT unverified[Title]" or Embryophyta: --p-query "txid3193[ORGN] AND (ITS OR Internal Transcribed Spacer) NOT environmental sample[Title] NOT environmental samples[Title] NOT …

-Cheers!
-Mike