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clemente-lab / mmeds-meta

A database for storing and analyzing omics data
https://mmeds.org
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Move to GreenGenes2 for Taxonomic reference #382

Open cleme opened 2 years ago

cleme commented 2 years ago

Is your feature request related to a problem? Please describe. Greengenes has not been updated since 2013, and while it remains highly popular (since it is default in Q2), we should explore alternatives.

Describe the solution you'd like Include option to run taxonomy with SILVA, as it seems to be updated regularly.

adamcantor22 commented 2 years ago

would love to be able to use the Taxonomy library for this to be able to easily switch between datasets. since this is currently scheduled for December release, that might be possible by then, yeah?

cleme commented 2 years ago

I am sure @mstapylton agrees with that timeline!

adamcantor22 commented 11 months ago

Repurposing this issue to be for migrating to GreenGenes2. GreenGenes2, due to how the qiime artifacts are created, requires using our more recent install of qiime (2022.11). We should consider migrating all analysis to that newer version, if we have to use it anyway.