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Our Work Infectious Disease Rapid Response

Resources

The Rapid Response Team provides metagenomic next-generation sequencing (mNGS) training and support to groups all over the world. Here you will find mNGS protocols and training materials that were developed in collaboration with the Genomics and Sequencing Platform at CZ Biohub and the CZ ID team at the Chan Zuckerberg Initiative.

Getting Started

Study Design

mNGS protocols

Enrichment and depletion

Sequencing

Quality Control

Analysis

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

Metagenomic next-generation sequencing (mNGS) protocols

Library Preparation for mNGS.

  • Library QC

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
  • FAQs

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

  • Overview
  • Quick guide to phylogenetic tree types
  • How to upload your data
  • FAQs
  • Genomic Epidemiology Learning Center

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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