QIIME 2 method section for publication


I am writing my manuscript but I have trouble in writing method section in regards to QIIME2.

I followed “Atacama soil microbiome” and Moving pictures” to process sequencing data. But since it is my first time to write manuscript with QIIME2, I have no idea of how to write the detail of the data process. So, could you please suggest any paper that I can refer to? And could you please let me know which paper I should cite for QIIME2?

Thank you in advance for your help.

Hi @scho73,
Good question!

See this post:

In addition to the citation information described in that post, you can also view references that you should cite for any individual artifact that you have generated (citations are shown for the last command used to generate that artifact, so you will need to do this for each artifact that you use in your analysis). To do this:

  1. View an artifact in https://view.qiime2.org/

  2. Click on the "Provenance" tab at the top-right of the screen:

  3. Below the ":qiime2: view" logo, click on the "citations" tab:

And you will get a list of references for the last command that was run to generate that artifact. Don't forget to do this for all artifacts that you use in your analysis (including intermediate artifacts like dada2 outputs) since it looks like right now only citations for terminal commands are displayed. Note that you can also look at the citation provenance in the artifacts in the tutorials, so it could be easier to just examine all steps of the tutorials you followed to see the intermediate citations, and then check your own artifacts for any additional analyses you performed.

Here is a list of methods/references that you may have used in your analysis, not including any additional analyses you may have used downstream (check those artifact citations!):

  1. QIIME 1 (Caporaso et al., 2010)
  2. dada2 (Callahan et al. 2016)
  3. deblur (Amir et al. 2017)
  4. OTU picking: vsearch (Rognes et al. 2016)
  5. Taxonomy classification: q2-feature-classifier (Bokulich et al., 2018)
  6. Greengenes (McDonald et al. 2012) or SILVA (Quast et al. 2013) databases

There will be others if you used any diversity analyses; alignment/phylogeny; or other plugins.

I hope that helps!


A QIIME 2 pre-print is now live and citable. Please see this post:

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