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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 CZ Biohub San Francisco and the Chan Zuckerberg Initiative.

Getting Started

Study Design

mNGS protocols

Enrichment and depletion

Sequencing

Quality Control

Analysis

Genomic Epidemiology

Additional Materials

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Getting Started

Metagenomic sequencing (mNGS): introduction and lab setup

Introduction to Illumina sequencing and data analysis for mNGS using CZ ID

A guide to BLAST

Study Design

mNGS: study design and sample preparation

Metagenomic next-generation sequencing (mNGS) protocols

Sample collection protocols

Illumina mNGS protocols

Oxford Nanopore mNGS protocols

Illumina library preparation for mNGS

Illumina library quality control

Enrichment and depletion methods

Overview

FLASH protocol

FLASH

DASH protocol

DASH publication

Guide RNA transcription (In Vitro Transcription for dgRNA V.2)

Sequencing

iSeq loading guide

MiSeq loading guide

Quality Control

Sample QC

Sequencing Run QC

Analysis

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

  • Overview
  • Quick guide to phylogenetic tree types
  • TheiaGenEpi user guides
  • FAQs

Genomic Epidemiology Learning Center

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
  • Season 2, Episode 1
  • Season 2, Episode 2
  • Season 2, Episode 3
  • Season 2, Episode 4
  • Season 2, Episode 5
  • Season 2, Episode 6
  • Season 2, Episode 7

Additional Materials

How to make your own SPRI beads

Sequencing SARS-CoV-2 for public health laboratories

  • SARS-CoV2 Sequencing Strategies
  • SARS-CoV-2 metagenomic sequencing by spiked primer enrichment (MSSPE), library prep protocol
  • SARS-CoV-2 ARTIC sequencing using Illumina, library prep protocol
  • Host transcriptome analyses for SARS-CoV2
  • SARS-CoV2 Genome QC & Phylogenetics

Scaling sequencing

A guide to BLAST

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Created and supported by the Chan Zuckerberg Initiative, the Chan Zuckerberg Biohub Network is a group of nonprofit research institutes that bring together physicians, scientists, and engineers with the goal of pursuing grand scientific challenges on 10- to 15-year time horizons. The CZ Biohub Network and CZI partner to understand the mysteries of the cell toward our joint mission to cure, prevent or manage all diseases by the end of the century.

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