Taxonomic assignment of feature IDs to reads

Welcome @Margreet! (to QIIME 2 and the forum) :tada:

QIIME 2 has a variety of plugins and methods for predicting taxonomic affiliations of sequences. q2-feature-classifier is the main plugin, with various methods to choose from... you can read the documentation at docs.qiime2.org for usage details (e.g., for training a naive Bayes classifier from a set of training sequences). In general if you are brand-new to QIIME 2 I recommend checking out the tutorials and other documentation there... it will be really useful for giving you an introduction to the different plugins available (as well as a description of what a "plugin" is if you are not yet aware).

You are in luck — @devonorourke recently put together the following tutorial AND a pre-trained COI classifier (scroll to the very bottom of the tutorial to get the classifier, the sequences and taxonomy used to train that classifier (e.g., in case you want to re-train it or use a non-sklearn classifier) or other intermediate files):

Good luck!

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