classifier for fungi data analysis

[AnaBanana (Ana)]

Hello everyone,

I am trying to analyse data from fungi from the genus Fusarium, I used the primers Fa 150 and Ra-2 to amplify 430bp of the elongation factor as done in Cobo-Diaz et al., 2019 (doi: 10.1093/femsec/fiz084). Does someone knows of a classifier I could use for this region in QIIME2 and perhaps a tutorial that I could follow in order to make the analysis work?

Thanks!!

[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: 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…

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 envi…

-Cheers!
-Mike

[AnaBanana (Ana)]

Many thanks Mike! This was a very helpful solution to create my own classifier for the elongation factor specific region!

Ana