CBW 2024 workshops

Introduction

Between May 27-30 2024 we ran workshops with Canadian Bioinformatics Workshops (CBW) at Memorial University in St John's, Newfoundland. These were split to Beginner (May 27-28) and Advanced (May 29-30) Microbiome Analysis. The Beginner Microbiome Analysis provided an introduction to marker gene analysis and was designed for those who had no prior experience in microbiome analysis, bioinformatics, or programming (full course outline). The Advanced Microbiome Analysis provided an introduction to read-based and assembly-based metagenomic data analysis and was designed for either those that already had some prior experience with microbiome data analysis and programming, or had also taken the Beginner Microbiome Analysis course (full course outline).

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

I have provided some additional information here 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 were provided with access to Amazon Web Services (AWS) servers/instances to use. These instances already had all of the programs and data that we were using for the tutorials pre-installed, and participants were given their own login information. These have been made available for anyone to launch for themselves, 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.

Beginner Microbiome Analysis

Module 1: Introduction to Sequencing Data Analysis

Morgan Langille & Robyn Wright

Module 2: Marker Gene Profiling

Robyn Wright & Monica Alvaro Fuss

Module 3: Microbiome Statistics and Visualizations

Morgan Langille & Monica Alvaro Fuss

Module 4: Functional Prediction and Additional Analyses

Morgan Langille & Robyn Wright

Advanced Microbiome Analysis

Module 1: Introduction to MGS and Read-Based Profiling

Morgan Langille & Ben Fished

Module 2: MAG Assembly and Binning

Robyn Wright

Module 3: Metagenomic Functional Annotation

Morgan Langille & Robyn Wright

Module 4: Advanced Microbiome Statistics

Monica Alvaro Fuss, Morgan Langille & Ben Fisher

Contact

Please feel free to post a question on the Microbiome Helper google group if you have any issues.
General comments or inquires about Microbiome Helper can be sent to [email protected].