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nf-core / ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2
https://nf-co.re/ampliseq
MIT License
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Add UNITE 9.0 databases #574

Closed prototaxites closed 1 year ago

prototaxites commented 1 year ago

Description of feature

The most recent UNITE version available in ampliseq is 8.3, which was released in May '21 - version 9.0 is available (https://unite.ut.ee/repository.php#panel5a, last release Nov '22).

Would be good to keep up-to-date with the latest taxonomy!

erikrikarddaniel commented 1 year ago

Description of feature

The most recent UNITE version available in ampliseq is 8.3, which was released in May '21 - version 9.0 is available (https://unite.ut.ee/repository.php#panel5a, last release Nov '22).

Would be good to keep up-to-date with the latest taxonomy!

Indeed. Do you fancy contributing this? Happy to help, please use the nf-core Slack channel #ampliseq channel for help.

prototaxites commented 1 year ago

Happy to add this (should be pretty straightforward) - will shoot a message in Slack about how to process the files as it looks like the pipeline doesn't download the release directly from UNITE.

jtangrot commented 1 year ago

I have now finished updating the SH files, needed for the addsh option, to UNITE 9.0, and I am preparing a PR with the new databases. I don't know if you did any work on the other "tracks", like the standard analysis with assignTaxonomy, or qiime @prototaxites? My initial tests have some problems with qiime classification and the unite-fungi version 9.0 (unite-alleuk works fine), qiime claims "this classifier does not support confidence values". Googling indicates this could be a formatting issue, but I find this unlikely as the unite-fungi file is just a subset of unite-alleuk, which works. Does anyone know what the issue could be?

jtangrot commented 1 year ago

UNITE 9.0 is now in dev, except for the QIIME version of unite-fungi.

d4straub commented 1 year ago

Seems solved?!