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Demo! UNITE v9.0 for qiime2-2023.2

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@colinbrislawn colinbrislawn released this 05 Mar 01:43
· 43 commits to main since this release
9.0-qiime2-2023.2-demo
225107a

⚠️ This is a public demo, and has not been validated. I am not affiliated with the UNITE team. Use at your own risk!

This is a classifier for version 9.0 of the UNITE database trained for use with Qiime2 2023.2. These can be used with q2-feature-classifier like those found on the Data resources page.

UNITE is licensed under CC BY-SA 4.0. If you use it, cite it! 🤝

Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2022): UNITE QIIME release for Fungi. Version 16.10.2022. UNITE Community <DOI GOES HERE>

DOIs for specific releases are listed here: https://unite.ut.ee/repository.php

Changes:

  • Update Qiime2 to 2023.2
  • Only include 99% and 'dynamic' thresholds (97% disabled by default)
  • Now uses already existing named conda environments. This means you will not get duplicate conda environments installed, but you will have to install Qiime2 first before running this pipeline. You can still have this pipeline manage your Qiime2 conda env, if you want.

There are two levels of classification provided here:

  • "99", which is 99% identity between taxa
  • "dynamic", which uses 97% to 99% identity between taxa, as individually recommended by experts in the field.

There are two taxa scopes:

  • "" Just Fungi
  • "all" All eukaryotes

There two versions, with and without an "s":

  • "" Includes singletons set as RefS (in dynamic files).
  • "s" Includes global and 97% singletons.
    (I'm not sure what that means.)

Notes on dates:

On the main UNITE download page, Version number 9.0 has a Release date of 2022-10-16.

However, that DOI leads to three, progressively newer files (webpage, api)

  • sh_qiime_release_16.10.2022.tgz
  • sh_qiime_release_27.10.2022.tgz
  • sh_qiime_release_29.11.2022.tgz

I've used the newest file (29.11.2022), which is why the file dates are newer than the release date.

All feedback is welcome! Please open an issue! ✅

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