Releases: colinbrislawn/unite-train
UNITE v10.0 v04.04.2024 for qiime2-2024.5
This is a classifier for Unite v10.0 Version 04.04.2024 trained for use with Qiime2 2024.5.
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 (2023): UNITE QIIME release for Fungi. Version 18.07.2023. UNITE Community <DOI GOES HERE>
DOIs for specific releases are listed here: https://unite.ut.ee/repository.php
Changes:
- Update to qiime-2024.5
There are three levels of classification provided here:
- "97", in which the database is clustered at 97% identity (not recommended!)
- "99", in which the database is clustered at 99% identity
- "dynamic", which uses 97% to 99% identity as individually recommended by experts
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)
All feedback is welcome! Please open an issue! ✅
UNITE v10.0 v04.04.2024 for qiime2-2024.2
This is a classifier for Unite v10.0 Version 04.04.2024 trained for use with Qiime2 2024.2.
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 (2024): UNITE QIIME release for Fungi. Version 04.04.2024. UNITE Community <DOI GOES HERE>
DOIs for specific releases are listed here: https://unite.ut.ee/repository.php
Changes:
- Update Unite to Version 10!
- Add 97% as requested in #8
There are three levels of classification provided here:
- "97", in which the database is clustered at 97% identity (not recommended!)
- "99", in which the database is clustered at 99% identity
- "dynamic", which uses 97% to 99% identity as individually recommended by experts
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)
All feedback is welcome! Please open an issue! ✅
UNITE v9.0 v25.07.2023 for qiime2-2024.2
This is a classifier for Unite v9.0 Version 18.07.2023 trained for use with Qiime2 2024.2.
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 (2023): UNITE QIIME release for Fungi. Version 18.07.2023. UNITE Community <DOI GOES HERE>
DOIs for specific releases are listed here: https://unite.ut.ee/repository.php
Changes:
- Update Qiime2 to version 2024.2
- This should work with any distribution (like amplicon & shotgun). If not, please open an issue! ✅
- Working to fix Release Date badge on main README.md
There are two levels of classification provided here:
- "99", in which the database is clustered at 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 (I may remove this in the future, see #5)
- "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 2023-07-18.
However, the notes and file name say 'Version 18.07.2023' which is when it was updated (webpage, api)
I'm using the newer file.
All feedback is welcome! Please open an issue! ✅
UNITE v9.0 v25.07.2023 for qiime2-2023.9
This is a classifier for Unite v9.0 Version 18.07.2023 trained for use with Qiime2 2023.9.
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 (2023): UNITE QIIME release for Fungi. Version 18.07.2023. UNITE Community <DOI GOES HERE>
DOIs for specific releases are listed here: https://unite.ut.ee/repository.php
Changes:
- Update Qiime2 to version 2023.9
- This should work with all three distributions: amplicon, shotgun, and tidy. If not, please open an issue! ✅
There are two levels of classification provided here:
- "99", in which the database is clustered at 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 2023-07-18.
However, the notes and file name say 'Version 25.07.2023' which is when it was updated (webpage, api)
I'm using the newer file.
All feedback is welcome! Please open an issue! ✅
UNITE v9.0 v25.07.2023 for qiime2-2023.7
This is a classifier for Unite v9.0 Version 18.07.2023 trained for use with Qiime2 2023.7.
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 18.07.2023. UNITE Community <DOI GOES HERE>
DOIs for specific releases are listed here: https://unite.ut.ee/repository.php
Changes:
- Update Qiime2 to version 2023.7
- Internal changes:
- Add basic benchmarks
- Change default cluster settings
- Import using new MixedCaseDNAFASTAFormat (thanks @mikerobeson!)
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 2023-07-18.
However, the notes and file name say 'Version 18.07.2023' which is when it was updated (webpage, api)
I'm using the newer file.
All feedback is welcome! Please open an issue! ✅
Contributors
Assets 12
Demo! UNITE v9.0 v25.07.2023 for qiime2-2023.5
This is a classifier for Unite v9.0 Version 25.07.2023 trained for use with Qiime2 2023.5.
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 18.07.2023. UNITE Community <DOI GOES HERE>
DOIs for specific releases are listed here: https://unite.ut.ee/repository.php
Changes:
- Update to Unite v9.0 to Version 25.07.2023
- That's right, Unite uses two version numbers for each release, and sometimes only one of them changes
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 2023-07-18.
However, the file name say 'Version 25.07.2023' which is when it was updated (webpage, api)
I'm using the newer file, which is why my version says 25.07.2023 and the DOI says 18.07.2023
All feedback is welcome! Please open an issue! ✅
Demo! UNITE v9.0 for qiime2-2023.5
This is a classifier for version 9.0 of the UNITE database trained for use with Qiime2 2023.5. 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 2023.5
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! ✅
Demo! UNITE v9.0 for qiime2-2023.2
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! ✅
Demo! UNITE v9.0 for qiime2-2022.11
This is a classifier for version 9.0 of the UNITE database trained for use with Qiime2 2022.11. 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 UNITE to 9.0
- Update Qiime2 to 2022.11
- New file name convention:
unite_ver9_dynamic_s_29.11.2022-Q2-2022.11.qza db_ version_ distance_ taxa scope_ file date- Qiime2-version.qza
There are three levels of classification provided here:
- "97", which is 97% identity between taxa
- "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 is also version with and without an "s":
- "" Includes singletons set as RefS (in dynamic files).
- "s" Includes global and 97% singletons.
- (I'm still not sure what that means.)
Notes on dates:
On the main UNITE download page, Version numer 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! ✅
Demo! qiime2-2022.8-v8.3
This is a classifier for version 8.3 of the UNITE database trained for use with qiime2-2022.8 (install guide, release notes).
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 (2021): UNITE QIIME release for Fungi 2. Version 10.05.2021. UNITE Community. https://doi.org/10.15156/BIO/1264763
Changes:
- Update Qiime2 to 2022.8
There are three levels of classification provided here:
- "97", which is 97% identity between taxa
- "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:
- "" Fungi
- "all" All eukaryotes
There is also version with and without an "s". (what does that mean?):
- "" Includes singletons set as RefS (in dynamic files).
- "s" Includes global and 97% singletons.
All feedback is welcome! Please open an issue! ✅