CZI-CABANA Joint Workshop: Microbiome Bioinformatics with QIIME 2


 Monday 5 Friday 9 October 2020


Virtual format -

Application opens: 

Tuesday 15 September 2020

Application deadline: 

Sunday 27 September 2020


Open application with selection


Greg Caporaso, Matthew Ryan Dillon

Registration fee: 

$50 USD general admission, free for Latin American trainees

Registration closed

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Dates additional information: 

This workshop will be taught between 08:00-14:00 UTC-7 for 5 days.

Course Overview

Members of the QIIME 2 team will teach a five-day online workshop on bioinformatics tools for microbiome science. This workshop will provide attendees with the foundation needed to begin using QIIME 2 to advance their own microbiome research projects. This will be accomplished by providing detailed in-depth “theory” lectures, hands-on interactive tutorials, guided discussion, and general question-and-answer sessions

The workshop will include lectures covering QIIME 2 usage and theory, and interactive work with QIIME 2 to perform microbiome analysis from raw sequence data through publication-quality statistics and visualizations. This workshop will also feature several opportunities for attendees to network with other researchers in the field, as well as with QIIME 2 developers and other experts.


Topics will include:

  • Introduction to QIIME 2
  • Core concepts
  • QIIME 2 types, formats, and metadata
  • Demultiplexing and quality control
  • Phylogenetic reconstruction
  • Measuring alpha and beta diversity
  • Importing and exporting data
  • Taxonomic analysis
  • Differential abundance
  • QIIME 2 plugin highlights

This online course will comprise a blend of pre-recorded and live lectures. Pre-recorded lectures will be made available prior to each day of the workshop, that way attendees with schedule conflicts can stay caught up with the material. There will also be interactive command-line based tutorial sessions, where attendees will perform microbiome analyses using QIIME 2, online.


This course is suitable for postgraduate wet-lab researchers and also bioinformaticians at graduate-level upwards within Latin America who are working with and/or generating their own microbiome datasets. Ideally your research or application is related to CABANA's challenge areas of sustainable food production, protection of biodiversity, or communicable diseases.


This workshop is part-funded by the CABANA project and has a maximum capacity of 50 trainees, 25 of which are for trainees within Latin America (excluding Chile and Uruguay due to GCRF grant conditions). If you are not currently employed within Latin America, you can still register for this course via general admission, please visit the QIIME workshop website for more details.

Early-stage researchers and researchers from underrepresented ethnic groups are especially encouraged to apply for this workshop.

Please note this course will be taught in English.


Software requirements

Before the workshop, please install the latest version of the Google Chrome web browser. If you don't have Google Chrome installed, get it here.

If you already have Google Chrome installed, make sure it is the latest version by following these instructions.

Next, install the Secure Shell app for Google Chrome.

After that, try opening this page to ensure that your browser is configured correctly to view Emperor plots. If you get a notice that the page cannot be opened, follow the instructions provided on that page and try the link again.


Preparing for the workshop

Students will use the Linux command line extensively during the hands-on portion of the workshop. We will not cover command-line usage in this workshop and thus it is strongly encouraged that you become familiar with the command line prior to the workshop.

The following resources are recommended to learn the command line. Depending on previous experience with the command line and level of technical expertise, it may take anywhere from a few hours to a few days to get comfortable using the command line. Thus, we recommend that students start working through this material as soon as possible, including the accompanying exercises.

  • Our cheat-sheet of command-line basics: The minimum working knowledge necessary for working with QIIME 2 on the command line.
  • Udacity Linux command line course (free): This course is pretty comprehensive and will take a few days to complete. Additionally, it shows users how to set up a virtual machine to run Linux commands in (this step is required for Windows users but can also be performed by Mac OS X and Linux users).
  • Software Carpentry Unix Shell introduction (free): This course is shorter than the Udacity course above, taking about 1.5 hours to complete. If you are on Windows, you will need access to a Linux machine (or virtual machine) to execute commands in. The Udacity course above will show you how to do this, or you can try out a Linux command line emulator (there are emulators available online). If you are using Mac OS X or Linux, you can alternatively use the Terminal program included with your operating system to execute commands in.

Learning outcomes

By the end of this course, participants should be able to:

  • Explain QIIME 2 types, formats and metadata.
  • Demultiplex data and perform quality control
  • Reconstruct basic phylogenetic trees
  • Measure alpha and beta diversity
  • Import and export data
  • Perform basic taxonomic and differential abundance analyses
  • Define various existing QIIME 2 plugins