Getting started with using QIIME 2#

If you’re new to QIIME 2, you may find it helpful to read q2book , another QIIME 2 JupyterBook which introduces concepts of the QIIME 2 bioinformatics platform. This will help you understand why QIIME works the way it does, discussing concepts including QIIME 2 archives (i.e., .qza and .qzv files), semantic types, plugins, and importing.

It’s not essential to have a complete grasp of all of the ideas in this section to use QIIME 2. But the more of this that you know, the more QIIME 2 will make sense to you, and the more benefit you’ll get out of learning and using the system.

Please pose any questions you have, on the tutorials that follow in this book, or on the ideas presented in q2book, on the QIIME 2 Forum

QIIME 2 View#

QIIME 2 View is a web-based viewer for .qza and .qzv files. If you’ve never visited QIIME 2 View, take a minute to go to the site now. This site allows for you to view QIIME 2 results on computers that don’t have QIIME 2 installed on them, and there are a few examples that you can look at in the gallery on that page. I use QIIME 2 View daily, for a few different situations. First, if I’m running analyses on a cluster computer than doesn’t provide a graphical interface, it’s a convenient way to view those results without having to load QIIME 2 on another computer. If I have a copy of a .qza or .qzv file on my local computer (e.g., if I copied it over from the cluster) I can navigate to QIIME 2 View, and drag-and-drop the file on the QIIME 2 View page to look at it. Another scenario where this is helpful is if when I’m sharing interactive QIIME 2 results with someone who doesn’t have QIIME 2 installed, for example a collaborator. I can send them .qzv files by email (or use the Dropbox sharing option on QIIME 2 View), and they can load and interact with the results on their computer.


When you’re using QIIME 2 View, your data isn’t uploaded to a server. Rather the site acts as an application launcher that allows you to view local files. This means that you don’t need to be concerned about data privacy issues with QIIME 2 View - the data never leaves your computer.