Resources
The Rapid Response Team provides pathogen genomics training and support to groups all over the world with a focus in metagenomics (mNGS) and genomic epidemiology. Here you will find protocols and training materials developed in collaboration with the Genomics and Infectious Disease teams at Biohub and the Chan Zuckerberg Initiative.
Key
Google Slides
Google Doc
Web Page
CZ ID: The free, cloud-based metagenomics platform for researchers
- Overview
- Guide to data analysis on CZ ID
- How to upload your data
- Guide to viral consensus genome generation from Amplicon sequencing data
- FAQs
TheiaGenEpi: An open source, free, no-code genomic epidemiology analysis platform for public health
The Applied Genomic Epidemiology Handbook
Essential Background Theory for Genomic Epidemiology
- Module 1: The overlapping timescales of pathogen evolution and transmission
- Module 2: From sequences to trees
- Module 3: Shared terminology for describing phylogenetic trees
- Module 4: Estimating evolutionary rates (molecular clocks) from sequence data
- Module 5: Interpreting and working with evolutionary rates
- Module 6: Using evolutionary rates to infer time trees
Practicing Gaining Epidemiological Insights from Genomic Data
- Genomic Epi Basics: Sequence alignments and molecular clocks
- Genomic Epi Basics: Practice reading phylogenetic trees
- Applying the mutation report to disease surveillance work
- Epi Insights Part I: Assessing linkages between COVID-19 cases
Genomic Epidemiology Seminar Series Recordings
- Season 1, Episode 1
- Season 1, Episode 2
- Season 1, Episode 3
- Season 1, Episode 4
- Season 1, Episode 5
- Season 1, Episode 6
- Season 1, Episode 7
- Season 1, Episode 8
- Season 1, Episode 9
- Season 1, Episode 10
- Season 1, Episode 11
- Season 1, Episode 12
- Season 1, Episode 13
- Season 1, Episode 14
- Season 1, Episode 15
How to make your own SPRI beads