train a sequence classifier on your own data

[timanix (Timur Yergaliyev)]

Hello!

@chupperts

From this point, is it possible to train a new classifier using my own sequences and taxonomy files, based on the taxonomy already assigned?

If you are asking about the technical possibility, then yes, you can train the classifier with your sequences or taxa.
However, I would not recommend this approach, as it limits the database to the scope of the previously annotated community. You can lose a lot of information!

@chupperts

Would it be better to create separate classifiers for each piglet age group (e.g., one for young piglets and another for adults), or is a single classifier sufficient for all age groups?

The single classifier would be better

@chupperts

Based on this, I wanted to prepare a new classifier using the following files from the Greengenes2 (2024) release: 2024.09.seqs.fna.qza and 2024.09.taxonomy.id.tsv.qza . With this classifier, I will be able to assign taxonomy to my data.

Looks like the best option to me!

Check out RESCRIPt for tutorials on how to train the classifier (though you need to adapt the commands for predownloaded GG2 sequences).

Or check if GG2 repo and this post have some insights.

Best,