how to reference the plugins used

I have read the instruction on the website on how to export the references of the plugin we used (in the provenance and citation option).
but it would be too much references and I checked in some papers that they do not cite all of these things.
I wanted to ask if anyone can help me to know how to cite the qiime plugins (permanova, shannon, observed features, evenness, faith phylogenetic tree, braycurtis, scenic plugin, taxa barplot, and picrust2)
Thank you very much

Hi @mohsen_ej ,

There are many software packages involved, and much effort by different groups (i.e., not just the QIIME 2 developers!). It is not just courtesy to the many scientists responsible... scientific integrity and basic ethics (and licensing laws!) would require that you cite the work of others when you use their methods or ideas... so in this regard there is never "too much".

Journals do often make restrictions on the number of citations allowed to print on the page... you should consult with the editors of the journal if this is the case. E.g., often methods sections are moved to the supplemental text and have their own references section.

But the methods still need to be properly cited.

There are many bad examples out there in the literature.

See this page for more details and an example (that covers some of the methods you mentioned):


thank you for your comprehensive explanation :pray: I'll go through them.

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