# when to use shogun

**URL:** https://forum.qiime2.org/t/when-to-use-shogun/24690
**Category:** Library Support
**Created:** [November 7, 2022, 9:27pm UTC](https://forum.qiime2.org/t/when-to-use-shogun/24690 "2022-11-07T21:27:42Z")
**Posts on this page:** 1
**Showing post:** 2

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### Author: ![colinbrislawn](https://forum.qiime2.org/user_avatar/forum.qiime2.org/colinbrislawn/32/6221_2.png) [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [November 8, 2022, 4:55pm UTC](https://forum.qiime2.org/t/when-to-use-shogun/24690/2 "2022-11-08T16:55:14Z")

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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However, it also looks like some of these plugins may be out of date at the moment.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](https://forum.qiime2.org/t/shotgun-sequence-analysis/24231/3) and this followup post:

> [@q2-sapienns: a plugin for loading HUMAnN3 and MetaPhlAn3 tables for downstream analysis in QIIME 2](https://forum.qiime2.org/t/q2-sapienns-a-plugin-for-loading-humann3-and-metaphlan3-tables-for-downstream-analysis-in-qiime-2/24306):
>
> Hi all, I have recently been doing some analysis of shotgun metagenomics data and wanted to run some downstream QIIME 2 analyses, including supervised classification and ordination, on tables that I generated with HUMAnN3 and MetaPhlAn3. This turned out to be useful for my work, so I wrapped this functionality up in a new plugin, [q2-sapienns](https://github.com/gregcaporaso/q2-sapienns). Importantly, q2-sapienns doesn't allow for running of HUMAnN3 or MetaPhlAn3 directly, but rather expects that you have generated gene family, pathway, or…

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

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