when to use shogun

I've looked through the QIIME2 tutorials, and I'm wondering at which point shogun should be implemented. For example, would I still dereplicate and cluster OTUs with QIIME, and then use Shogun for the classifier step?

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Hello again Rachel,

I think many of the shotgun tools work directly on quality filtered reads, no denoising or feature table creation required.

However, it also looks like some of these plugins may be out of date at the moment. See this post and this followup post:

I would also like to find an updated best-practices guide for shotgun analysis with Qiime2 in 2022.

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Hi @Rachel_Keuler and @colinbrislawn,
I think @colinbrislawn's post and the links he shares are the best we can offer for shotgun workflows in QIIME 2 right now.

I would also like to find an updated best-practices guide for shotgun analysis with Qiime2 in 2022.

It won't be in 2022, but we are expecting new shotgun plugins and documentation in the first quarter of 2023. These will be in "alpha release" at that time, meaning that they'll be fully usable, but we'll caution users to be on the lookout for anything that doesn't look right, and that they may be a little rough around the edges.

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