CZI-CABANA Microbiome Bioinformatics with QIIME 2 Workshop (sold out)

Oct. 5, 2020 - Oct. 9, 2020

General Admission has sold out, sorry for the inconvenience


Members of the QIIME 2 team will teach a five-day online workshop on bioinformatics tools for microbiome science. 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
  • And more!

Please save the dates for:

  • October 5th - October 9th, 2020
  • Sessions will begin at 8a and end at 2p daily, UTC-7 (3p-9p UTC+0)

Registration Information

We are providing three different attendance options:

  • Option 1: General admission tickets will be available starting September 16th
  • Option 2: CABANA tickets will be available starting September 15th, the application deadline is September 27th.
  • Option 3: Free viewing will be available for any interested attendee - no need to apply, just show up day-of (details to follow)!

If you previously reached out to us about a “purchasing power” discount, please watch out for an email from us with your discount code, you will use that to apply for Option 1 (General Admission). We will not be able to accept any more purchasing power requests after general admission sales begin.

Additional details about each option are discussed below:

Option 1: General Admission

We have received significant pre-sale inquiries - in order to provide a fair and balanced opportunity to attend, a tickets will be made available in batches, on predetermined and staggered schedule:

  • Wednesday, 9/16: 12:00, UTC -8
  • ~~Thursday, 9/17: 12:00, UTC -4~~
  • ~~Friday, 9/18: 12:00, UTC~~
  • ~~Saturday, 9/19: 12:00, UTC +3~~
  • ~~Sunday, 9/20: 12:00, UTC +6~~
  • ~~Monday, 9/21: 12:00, UTC +9~~
  • ~~Tuesday, 9/22: 12:00, UTC +12~~

If tickets sell out of a batch, more tickets will become available at the next batch start time. As well, we are offering a “free viewing” option (more details below), in case you aren't able to purchase tickets in any of the batches listed above.

Update: General admission has sold out, please see for more details.

Option 2: CABANA

We are really excited to announce that we are teaming up with the great folks with the CABANA program to provide discounted options for attendees based in Latin America. Applications will be accepted from September 15th through September 27th. For more information, please visit

Option 3: Free Viewing

The workshop will be simulcast live to YouTube! We will provide additional details the week before the workshop begins, so check back here in a few weeks. In the meantime, please install QIIME 2 so that you can follow along on your own (free viewing attendees will not have access to the shared workshop server used for the interactive tutorial commands we will run as a group).

Pre-recorded material will only be available to General Admission and CABANA attendees (and will only be available for a limited time during the week of the workshop). We hope to offer a fully standalone ad hoc online course soon (hopefully some time in 2021 - we will announce more details as we develop the course).

Purchasing Power Discounts

Purchasing power discounts are no longer available for this workshop.


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. We will also host many live question-and-answer sessions, as well as general discussion sessions.

Required software

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.

Check us out on the QIIME 2 Forum (link) for questions and general discussion about this workshop. Hope to see you there!

Register Now!

Each ticket purchased as part of an order will need a unique email address (these will be collected on the next step).

Ticket Quantity Rate Type Price
General Admission 50.00 USD Sold Out

Questions? Comments? Contact us.