IDTAXA: : a novel approach for accurate taxonomic classification of microbiome sequences

(M R ) #1

What are your opinion about IDTAXA (https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0521-5)?

According to this publication it is slightly better to Qiime2 features-classifier and other taxonomic classifiers, with less mis-classifications, but mostly less over-classifications. It’s also now the recommended taxonomic classifier in the DADA2 tutorial.
What are your thoughts? And should this method be included in a future release of Qiime2?

(Nicholas Bokulich) #2

Looks like a promising method, though the performance does not appear dramatically different from other classification methods (incl. QIIME 2’s vanilla naive bayes classifier, which performs quite well by their benchmark).

We would love to have the authors of IDTAXA write a plugin for their method, or consider adding it as an action to q2-feature-classifier (which already contains a few different classification methods). The more (methods) the merrier!

(M R ) #3

Dear Nicholas,

Thank you very much for your reply.

I agree with you that it does not blow the default qiime2 feature classifier out of the water at all. The performance increase seems to be minor.
This minimal increase in performance, but mainly because I would have to run it outside of Qiime2, are the reasons why I don’t think it’s worth it for me to switch. I’m happy with how my Qiime2 pipeline is set up at the moment. It might become more interesting if and when they decide to develop a Qiime2 plugin.

Cheers,

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