Qiime2 performance multi user

[Nicholas_Bokulich]

@arwqiime

Would you expect a reduction of server load (temporary data and or RAM), if I would extract the reference sequences to the 515-907 region only?

Yes, almost definitely

@arwqiime

The classifier of the 515-806 region is only 30% in size of the full classifier.

Note that 515-806 does not hit 18S (I think), so you might not see as much of a reduction in size, but something similar.

So do it! Faster to train, faster to classify.

Trimming to the same primers that you are using should also yield a slight increase in accuracy; you can test and compare classification performance with trimmed vs. untrimmed sequences using RESCRIPt:

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 construc…