CBW-IMPACTT Microbiome Analysis 2023
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 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 8: Setting Up a Clinical Microbiome Study
Anita Kozyrskyj
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