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Rationale and background:

QIIME (canonically pronounced chime)Quantitative Insights Into Microbial Ecology (

J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Pena, Julia K Goodrich, Jeffrey I Gordon, Gavin A Huttley, Scott T Kelley, Dan Knights, Jeremy E Koenig, Ruth E Ley, Catherine A Lozupone, Daniel McDonald, Brian D Muegge, Meg Pirrung, Jens Reeder, Joel R Sevinsky, Peter J Turnbaugh, William A Walters, Jeremy Widmann, Tanya Yatsunenko, Jesse Zaneveld and Rob Knight; Nature Methods, 2010; doi:10.1038/nmeth.f.303

QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on the Illumina or other platforms through publication quality graphics and statistics. This includes demultiplexing and quality filtering, OTU picking, taxonomic assignment, and phylogenetic reconstruction, and diversity analyses and visualizations. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples.


This tutorial will orient you to using the QIIME software package (version 1.9.1) installed on Atmosphere. This particular demo is adapted from the Illumina tutorial on the QIIME site. 

This tutorial will take users through steps of:

  1. Launching the QIIME-1.9.1 Atmosphere image
  2. Running QIIME-1.9.1 on an test data 

Please work through the tutorial and add your comments on the bottom of this page. Or send comments per email to Thank you.

Learn about allocations


Learn about CyVerse's allocation policies here.

Part 1: Connect to a Jupyter notebook on Atmosphere Image (Virtual Machine)

Step 1. Go to and log in with your CyVerse credentials.

Step 2. Click on the Launch New Instance button and search for Qiime-1.9.1

Step 3. Select the image Qiime-1.9.1 and click Launch Instance. It will take ~10-15 minutes for the cloud instance to be launched. 

Note: Instances can be configured for different amounts of CPU, memory, and storage depending on user needs.  This tutorial can be accomplished with the small instance size, medium1 (4 CPUs, 8 GB memory, 80 GB root)

Step 4. Launch Jupyter notebook on the Atmosphere image for running Qiime 1.9.1

Open the Terminal.  Add the ssh details along with your IP address to connect the instance through the terminal. Remember to put your actually iPlant username in place of the text 'username' and 'IPaddress' in this next line of code:

Run Jupyter Notebook command for launching Jupyter notebook.


Do not copy and paste the above link as that link is specific to my instance. Copy your own link

After you copy the link on to the browser. Click the "New" tab and select Python 2 kernel for running QIIME 1.9.1 which will open a Jupyter Notebook in a different tab




If you want to run the Qiime 1.9.1 on Atmosphere without Jupyter notebook you can do so using this protocol - QIIME-1.9.1 Using Atmosphere



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