Citation for trained greengene reference tree

User Support
1

Hi,
I downloaded and used the reference tree below (qiime2 trained taxonomic classifier using greengene). I am wondering how to cite this reference tree. Can you please advise?

"sepp-refs-gg-13-8.qza"
"https://data.qiime2.org/2021.4/common/sepp-refs-gg-13-8.qza"

I looked in qiim2 & github for a recommended citation, but it seems, I can't find one.
Qiime2 Doc >> Data resources >>Taxonomy classifiers for use with q2-feature-classifier
Qiime2 library >> # q2-fragment-insertion

Thank you!

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2

Hi @AYK ,

Do you want a citation for the SEPP reference tree, or for a trained taxonomic classifier?

The citations for this would be associated with the q2-fragment-insertion plugin. You can check those directly by typing this into your terminal:

qiime fragment-insertion --citations

The citations for the pretrained classifiers are mentioned on the "data resources" page where you download them:
https://docs.qiime2.org/2022.2/data-resources/

good luck!

1 Like
3

Thank you for your prompt reply.

There is no citation for the pertained classifier of SEPP reference databases (Greengenes 13_8 SEPP reference database), At the very bottom of the page Data resources — QIIME 2 2022.2.0 documentation.

Under SEPP reference databases >>> The link SEPP-Refs project >>> there is no citation in the Github page.

Please advice. Thank you

5

You can also inspect the citations in the artifact itself (same as for any artifact):

qiime tools citations sepp-refs-gg-13-8.qza
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