Functional Databases in QIIME 2

I can’t wait to try out the new VM when my computer finally downloads it!
As for databases, is there any possible way for a functional database to be imported into QIIME2 to use for the feature-classifier plugin? I found this really cool one that includes functional annotations for prokaryotic taxa.

Here is the link to the paper for the database:

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Good afternoon Liyah,

What kind of data are you processing? If you are using amplicons, I think you best bet would be to process your data using Qiime 2, export it, then analysis it with MACADAM as they described in the paper.

Or get the authors to make a Qiime 2 plugin for MACADAM! :wink: :qiime2:

Colin

P.S. There is a plugin called PICRUSt2 that predicts functional metagenomics from 16S data, and this one does have a Qiime2 plugin! Check out the tutorial on using PICRUSt! :pie:

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Hello, Colin,

I am using NextGen Illumina amplicons, and I am currently trying to write a Python script that accepts whole taxonomy TSV files as input (as it is now, I can only search a single taxa at a time). It would be awesome for a MACADAM plugin for QIIME2 to be made, if only to streamline the whole process. I will at least try out PICRUSt before going any further with that proposal, though. Thank you for your help!

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I agree! Maybe you or the MACADAM developers would be interested in writing a q2-MACADAM plugin? Let us know and we can help point you in the right direction to get started with plugin development!

I am definitely interested in writing a QIIME2 plugin for MACADAM, but I will reach out to the MACADAM developers for their input before doing anything for it. While I await their response, I would be delighted to receive advice and instructional direction on plugin development so that I can acquire the skill!

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Glad to hear that you are interested! It will be awesome to see a MACADAM plugin!

Developer documentation is here: https://dev.qiime2.org/latest/

In particular see the tutorials here: https://dev.qiime2.org/latest/tutorials/

That includes a beginner’s tutorial that @cduvallet put together a while back that is useful for anyone tackling their first QIIME 2 plugin!

In addition to announcing the forum and writing a tutorial on this forum, you should also be aware of the q2 Library as a clearing house for hosting information about q2 plugins: https://library.qiime2.org/

And of course get in touch on this forum with any specific questions (or even just more questions about getting started) — e.g., I can imagine you may have questions about appropriate semantic types for the inputs/outputs of MACADAM. Using the developers channel on this forum would be a great place to get help.

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