Training classifier for taxonomic analysis

[colinbrislawn (Colin J Brislawn)]

Hello Linda,

@Linda_Abenaim

I'll explain my work to you: I'm trying to analyse the intestinal microbiome of an insect species raised on a control diet and a treated diet to understand if there are any differences of bacterial community.

This sounds like a great project!

Have you tried using Greengenes2 with non-v4-16s, as shown in the main tutorial?

EDIT: This does not make ASVs from your data like other pipelines. Instead, it directly compares your reads against the GG2 database entries, which already have a taxonomy.

Simply counting database hits is also known as 'closed-ref-clustering'.
This has very different tradeoffs than denoising -> taxonomy inference.

Introducing Greengenes2 2022.10

Introduction We are excited to announce a new release of the Greengenes database, full redesigned from the ground up, backed by whole genomes, with a focus on harmonizing 16S rRNA and shotgun metagenomic datasets. We're calling the new database Greengenes2 due to substantial changes in the design. However, like the original Greengenes, it relies on a de novo phylogeny, and expresses a taxonomy that is derived from the phylogeny. The focus of this forum post is on how to use the new Greengenes2…

While GG2 should work well with a Naive Bayes classifier, using the GG2 plugin
qiime greengenes2 non-v4-16s
is a great place to start and provides a point of comparison.

Keep us posted!