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Microbiome Analysis
Workshop Pages for Students
CBW-IMPACTT Microbiome Analysis 2023
/site_images/CBW_Metagenome_icon.jpg
Microbiome Analysis
Microbiome Analysis
3 days

Welcome

The course schedule can be found here. To be sure everyone can smoothly connect to AWS, we will be holding a virtual office hour on July 4, 2023 from 2-3pm MST. It is in a drop-in format and attendance is highly encouraged.

Meet your faculty here

Pre-Workshop Materials

Pre-work including programs to install can be found here

AWS Module

Connecting and properly using a cloud computing cluster at the CBW here

Class Photo

Microbiome Analysis Class of 2023

Day 1

Welcome

John Parkinson

Module 1: Introduction

John Parkinson

Module 1 Lecture Slides

Module 2: Marker Gene Taxonomic Analysis (16S)

Morgan Langille

Module 2 Lecture Slides
Module 2 Lab
Module 2 Lab Answers

Module 3: Microbiome Statistics and Visualizations

Hena Ramay

Module 3 Lecture Slides
Module 3 Lab
Module 3 Lab Answers

Day 2

Module 4: Intro to MGS

Morgan Langille

Module 4 Lecture Slides
Module 4 Lab
Module 4 Lab Answers

Module 5: Metagenome Assembly & MAGs

Laura Sycuro

Module 5 Lecture Slides
Module 5 Lab

Day 3

Module 6: Metatranscriptomics

John Parkinson

Module 6 Lecture Slides
Module 6 Lab
Module 6 Lab Answers

Module 7: Sample Collection and Biases

Laura Sycuro

Module 7 Lecture Slides

Module 8: Setting Up a Clinical Microbiome Study

Anita Kozyrskyj

Module 8 Lecture Slides

Post-Workshop Materials

CourseData

Note that some of these files are quite large. If you have issues downloading them, try copying the link address, opening a new blank tab, and entering the URL into the new tab's address bar. If that fails, contact us at support@bioinformatics.ca.

AMI

We have made our AWS AMI (Amazon Machine Image) publicly available. To launch your own instance, follow the instructions provided by Amazon on how to launch an EC2 instance from a custom Amazon Machine Image. Please note that you will need an AWS account to proceed, and that you will need to upload the CourseData files yourself.

Here are the details of the AMI:

  • AWS Region: us-east-1 (N. Virgina)
  • AMI type: public image
  • AMI name: CBW_MIC_230702
  • AMI ID: ami-0daae6899f80e066f

If you want to create and activate a new AWS account, please follow the instructions provided by Amazon.

Software

conda

Tools used in the workshop were installed by conda environment. Install Miniconda by following the instructoion at Miniconda official site. Here is an example to install rgi.

rgi

conda create --name rgi --channel conda-forge --channel bioconda --channel defaults rgi