How do I use a pretrained classifier?

[colinbrislawn (Colin J Brislawn)]

Good evening!

Welcome to the forums!

You are on the right track and asking all the right questions! First, check out the RESCRIPt tutorial, which is the most complete overview of this process.

@BioHazard_Dragon

Do I need to extract region-specific reads and dereplicate first

Both are good ideas, and RESCRIPt will help you do both

Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt

Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. RESCRIPt RESCRIPt (REference Sequence annotation and CuRatIon Pipeline) is a python package and QIIME 2 plugin for formatting, managing, and manipulating sequence reference databases. This package was designed for compiling, manipulating, and evaluating sequence reference databases from SILVA, NCBI, Greengenes, GTDB, and other sources, and for constru…

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@BioHazard_Dragon

4. Is there a less resource-hungry alternative to the classify-sklearn step to get the taxonomy file?

Yes, you can avoid the pretraining with a top-hit LCA classifier like classify-consensus-vsearch . All good options!

I'm afraid I've given you much to consider without answering each of your questions. If you have more questions about LCA classifiers or how to use RESCRIPt, let me know.