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Adding the new Greengenes2 database for classification #658
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Hi there, Greengenes2 was discussed in https://nfcore.slack.com/archives/CEA7TBJGJ/p1690539708378009 & https://nfcore.slack.com/archives/CEA7TBJGJ/p1678204777328909. Using I hope for the integration of Greengenes2 for DADA2 classifications, that should solve all preprocessing and make the db integration relatively easy to add here, including an upload to Zenodo which is much preferred to a university DB. Greengenes2 was said to be "soon-ish" provided as DADA2 database in Zenodo, see benjjneb/dada2#1680 and benjjneb/dada2#1829. |
Greengenes2 support is now for QIIME2 available in the dev branch and will be in the next release. I dont close that issue though because there is still no news for DADA2 (or I missed it). |
Hi Daniel.
Thank you for the update. I do see greengenes2 in the github page but it
doesnt show as one of the parameter options on your nextflow page. Just
informing you. I havent used it yet but I plan to very soon.
Best regards,
Ali
…On Fri, Jan 12, 2024 at 12:04 AM Daniel Straub ***@***.***> wrote:
Greengenes2 support is now for QIIME2 available in the dev branch and will
be in the next release. I dont close that issue though because there is
still no news for DADA2 (or I missed it).
—
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Description of feature
Greengenes2 recently came out. Greengenes2 is a new release of the Greengenes database that has been redesigned from the ground up and backed by whole genomes, focusing on harmonizing 16S rRNA and shotgun metagenomic datasets. It is also
much larger than past resources in its phylogenetic coverage, as compared to SILVA, Greengenes and GTDB. It would be great to add this database as an optional feature for classifying sequences. Usage instructions are below. It has a QIIME 2 plugin. Notice that the approaches to classify sequences is different between V4 and non-V4 sequences.
Paper: https://www.nature.com/articles/s41587-023-01845-1
How to use it: https://forum.qiime2.org/t/introducing-greengenes2-2022-10/25291
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