Taxonomic discrepancy with Greengenes, Silva and NCBI

Hi @Marisa_Tello_Martin,

You are using a very old version of QIIME 2 (2020.8). I'd strongly recommend installing the latest version (2024.10) as a separate environment rather than trying to "update" the existing one. There are many improvements and additional functionality in the latest version. This is one of the benefits of conda environments, you can keep multiple versions of QIIME on your system and just activate the version you need. :slight_smile:

You can install Greengenes2 from here. More details are here.

You can use the RESCRIPt plugin to download and curate SILVA, GTDB, & RDP databases. Note this plugin comes with QIIME 2. See the GitHub page for more tutorials.

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