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University of Wisconsin–Madison

Bioinformatics Resource Center

The UW-Madison Biotechnology Center is currently open and following the university's COVID-19 Response regarding campus operations.

Microbiome analysis using QIIME2

2020 dates:

* February 19, 9:00am-4:00pm 

Location: Biotechnology Center, room 1360

LIMITED to 12 participants - (3 minimum)

REGISTER: use Google Calendar link to register on chosen date


This workshop will cover amplicon-based microbiome analysis using the QIIME2. This all-day workshop will consist of lectures and hands on training to analyze from raw dataset through publication-quality statistics and visualizations.

Participants are expected to have a basic knowledge of the Linux environment and a basic understanding of statistical methods.


The QIIME2 software will be used via line command method.
Must be comfortable with the Linux command line (bash shell) and familiar with basic Linux commands. 

Bring a WiFi capable laptop.

Set up proper connection software:

  1. Mac: XQuartz. This is semi-optional and for few if any graphics displays. Terminal is already installed on a Mac.
  2. Windows-PC: MobaXterm. Preferably choose the Portable edition over the installed edition for best results.

Optional for files transfer with a GUI:

  1. Cyberduck (, Mac/PC/Linux); 
  2. Alternative: WinSCP for Windows or the multi-platform version WinSCP crossover Trial-version.

Fee: $175 / seat


Sailendharan Sudakaran, Ph.D., Madison Microbiome Hub Manager / Multi Omics Hub Coordinator

Previous instructors:

none - This is a new workshop.

*No-show Policy*

To avoid charges all cancellation need to be notified 72 hours in advance.