q2-sapienns: a plugin for loading HUMAnN3 and MetaPhlAn3 tables for downstream analysis in QIIME 2

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.

Importantly, q2-sapienns doesn't allow for running of HUMAnN3 or MetaPhlAn3 directly, but rather expects that you have generated gene family, pathway, or taxonomy tables with those tools, and that you want to use them with QIIME 2. This should work on tables that contain only a single sample, or merged tables that contain many samples.

Installation and usage instructions can be found in the project's README.

I've used this in my own work now, and have performed extensive unit testing of the functionality, but it hasn't been widely tested in the wild yet. Treat this as "beta" software, and let me know if you discover any issues, either here or on the project's issue tracker.

Finally, I don't know yet if this all works with HUMAnN3.5 or MetaPhlAn4. I haven't had a chance to try those out yet. If the file formats haven't changed, this plugin should work just fine, but if you are using those most recent versions just be aware that q2-sapienns hasn't been tested with them yet. I'll be interested in hearing how it works with HUMAnN3.5 and/or MetaPhlAn4 so please feel free to share your experiences here.

I hope this is useful - enjoy!