CBW 2025 workshops - LangilleLab/microbiome_helper GitHub Wiki

Between May 26-30 2025 we are running workshops with Canadian Bioinformatics Workshops (CBW) at UBC in Vancouver, BC. These are split to Beginner (May 26-27) and Advanced (May 29-30) Microbiome Analysis. The Beginner Microbiome Analysis provides an introduction to marker gene analysis and has been designed for those who have no prior experience in microbiome analysis, bioinformatics, or programming (full course outline). The Advanced Microbiome Analysis provides an introduction to read-based and assembly-based metagenomic data analysis and has been designed for either those that already have some prior experience with microbiome data analysis and programming, or are also taking the Beginner Microbiome Analysis course (full course outline).

All course materials CBW makes all course materials and lectures available online after the workshops finish:

Beginner Microbiome Analysis Advanced Microbiome Analysis

These workshops will be similar to the CBW 2024 workshops that we ran. On that linked page, I provided some additional information and links to each of the module components to explain this for anyone that didn't attend the CBW workshop.

Introduction to Unix

As part of the workshop we held an initial Intro to Unix session before the workshop. If you do not have any previous experience with Unix/Command Line, I recommend first running through this page: Introduction to Unix

Amazon instances

During the workshops, participants will be provided with access to Amazon Web Services (AWS) servers/instances to use. These instances already have all of the programs and data that we were using for the tutorials pre-installed, and participants will be given their own login information. These will be made available for anyone to launch for themselves after the workshops, but you will need your own AWS account to do this, and Amazon does charge a small amount for this. There are some brief instructions on doing this within the CBW Beginner and Advanced pages, but I have written some more comprehensive instructions: Setting up an AWS instance with the CBW AMI

The Amazon Machine Images (AMIs) are essentially copies of all of the programs installed and data present on a server, so that you can launch this for yourself without needing to install anything. It is like creating a backup of your laptop so that you can access all of the same programs and data without needing to do anything.

Once you have set up an AWS account and launched the instance, you can work through the tutorial materials. I have linked all of them here for convenience.