Our Work Research Groups Rapid Response

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

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

TheiaGenEpi: An open source, free, no-code genomic epidemiology analysis platform for public health

Genomic Epidemiology Learning Center

The Applied Genomic Epidemiology Handbook

Essential Background Theory for Genomic Epidemiology

Practicing Gaining Epidemiological Insights from Genomic Data

Additional Materials

How to make your own SPRI beads

Sequencing SARS-CoV-2 for public health laboratories

Scaling sequencing

A guide to BLAST

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