Jump to Section:
About the materials
These materials (lectures & hands-on activities) can be used to train students on metagenomic analysis using CZ ID's platform. The target audience is those who are new to metagenomics (mNGS), including wet lab scientists, graduate students, and those interested in mNGS data interpretation.
What is CZ ID?
CZ ID is a free, open-source, no-code analysis platform for analyzing sequencing data. Researchers from anywhere in the world can analyze their data straight from their laptops, regardless of computational power or bioinformatic skills. CZ ID's publication can be found here.
CZ ID hosts four pipelines or analysis modules:
Module | Input data | Supported sequencing technology |
Metagenomics (mNGS) |
Shotgun (or random) data
Note: Module is NOT meant to process amplicon data (e.g., 16S, 18S, ITS) |
Illumina & Nanopore |
Antimicrobial resistance | Whole genome sequencing & mNGS | Illumina |
SARS-CoV-2 | Amplicon sequencing | Illumina & Nanopore |
Viral consensus genome | Amplicon sequencing & WGS | Illumina |
CZ ID's web application provides visualizations and downstream analyses to help the user interpret their data.
Training Preparation
Creating CZ ID Accounts
There are two options for setting up accounts in preparation for a training or workshop.
- Option 1: Create a demo account for the entire class to use. This option is ideal if you are planning on using public datasets. Click here for instructions on how to create a free CZ ID account that you can use for the entire class (you can share the login credentials during the training).
- Option 2: Have each participant set up an individual account. This option is ideal if students will be uploading their own data. Share instructions for how to create a free CZ ID account (found here) with every participant so they can create accounts prior to the training.
Datasets for Training
The training materials and syllabi below focus on how to interpret mNGS results. Keep in mind that no matter which dataset you decide to use for training, the core tenets of mNGS interpretation are the same.
Dataset | Sample # | Description | What can be found? | Publication |
Medical Detectives | 17 | Mix of samples from mystery illness projects. Pathogens are straightforward to identify. | Bacterial, viral, & eukaryotic pathogens | |
RNA-seq of SC2 and other respiratory viruses | 48 | Subset of samples looking at host gene expression in patients with SC2 compared to other viruses. Nice to pair with host gene expression training | SARS-CoV-2 & viral pathogens | Upper airway gene expression reveals suppressed immune responses to SARS-CoV-2 compared with other respiratory viruses |
Mosquito dataset | 35 | RNA-seq of single mosquitoes. | Novel viruses, animal pathogens, endosymbionts | Single mosquito metatranscriptomics identifies vectors, emerging pathogens and reservoirs in one assay |
Training Personnel
Depending on the workshop size, you will need teaching assistants (TAs) to help with hands-on activities, including navigating CZ ID, troubleshooting, and answering any questions that come up.
- <10 students, you can probably run the course with one TA, but having another person available would be helpful to answer student questions and help students follow along during hands-on activities.
- 10 - 20 students, have at least two TAs available to help with hands-on activities
- >20 students, have at least four TAs to help with hands-on activities.
Training materials
Below we provided training materials for one- or multi-day workshops. The table below contains full course materials. Download, edit, and reconfigure the materials as needed.
Use | Syllabus & materials | Data analysis | Number of students |
One-day workshop | One-day Workshop syllabus | Public dataset | 10 or more students |
Multi-day workshop | Multi-day mNGS syllabus | Public + own dataset | < 10 students |
You can also add additional materials to the existing syllabi. Below are some case studies with worksheets that can be used to tie all of the learnings together. This is especially nice if students do not have their own data to work with.
Case studies | Dataset | Worksheet | Publication |
Pneumonia | Pneumonia (Sample Report) | Case study: Pneumonia.docx | https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(21)00357-8/fulltext |
Meningitis | Meningitis (Heatmap) | Case Study: meningitis | |
Enteric Infection | Enteric Infection (Heatmap) | Case Study: Enteric disease |
Additional Resources
- ⚒ Guide for mNGS data analysis: Analysis guide that will walk you through what to do after uploading your mNGS data to CZ ID.
- Reference tables and worksheets: Tables with metric definitions and worksheets to work through mNGS data analysis.
- Rapid response team training materials: Slide decks describing mNGS experimental design and wet-lab protocols.
- CZ ID Help Center: Includes how-to guides that cover all things CZ ID, from uploading samples to analysis to downloading files.
- Glossary of important mNGS terms
Questions or Feedback?
Please email us at help@czid.org
Comments
0 comments
Article is closed for comments.