Citing QIIME and other tools with in the QIIME

Hello All
Thanks to the QIIME forum, finally I am almost done with the analysis after a month long hard work and restless days.
Thank for the support all the way.
No coming to the point, how to cite the QIIME, do I need to site each tool separately.
Second do I need to mention each of the step of the analysis. and third the most important. How can I know which pipeline have been used DADA2 and Deblur.
in My case I just imported the files and started closed reference clustering, after obtaining the sequencing from agency and after demultiplexing the files in QIIME1.
Please suggest.

Great question, @divyaprince321! Thanks for asking.
These questions are answered at length in the "Citing QIIME 2" section of the documentation. I'll provide some short answers below with targeted links.

QIIME 2 is not a single tool, but a platform that brings together published work from different contributors around the world. Because a QIIME 2 analysis relies on many people's research, you should include all relevant citations in your publications. It sounds like you also used QIIME 1. Here's the appropriate reference for citing QIIME 1; this should also be included.

Because it's possible to perform many different types of analysis with QIIME 2, providing an overview of which methods you chose to use (and how) is the only way for your reviewers/readers to understand your unique approach. Here's one example of how your methods section could look.

QIIME 2 automatically tracks the methods you used to generate your results. We call it "automatic decentralized provenance tracking", and it's one of the coolest things about QIIME 2.

Open any Artifact or Visualization with q2view, and click on the "Provenance" tab to see a graph of how that Artifact/Visualization was created. Click the circles or boxes for all the details.

The data for this taxa bar plot, for example, was denoised using DADA2. You can use the same tools to view citations relevant to your results. There's a detailed walkthrough here.

You will have to gather the citations from multiple Artifacts in order to fully and accurately represent your research. The third-party tool qax can simplify this process significantly. We hope to include similar tooling in qiime tools in the not-too-distant future.

Good luck with your publications!
Chris :paw_prints:

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Thanks Chris
I got it, however I have a doubt that is what I want you to please clear a bit
My case I just imported the files and started closed reference clustering, how can I know which pipeline I have used.

QIIME 2 doesn’t have fixed “pipelines”, @divyaprince321, just some common combinations of tools that people often use. There’s just too much functionality and flexibility for that idea to apply here, IMO. Even “simple” studies often rely on many, many statistical and computational tools, and those may need to be applied in slightly different ways for each study.

When you imported files, you used tools that research software engineers spent years developing. When you used closed-reference clustering, you used techniques developed by other research teams. When you investigate diversity, community change, community taxonomic profile, or differential abundance, the commands you run use formulae and algorithms from other important research publications.

Look at your results’ provenance, as I described above. They contain literally all the details you need about which tools you used, what citations you need to reference, etc. Documenting the tools you used may take you a little while, but crediting the research you rely on is important. After all, we couldn’t do this work without them. Tools like qax (mentioned above) can help streamline the process of gathering citations, and the QIIME 2 team is working on other tools that should make things even easier in the future.

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