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.
Lab Protocols
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Metagenomic next-generation sequencing (mNGS) protocols.
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SARS-CoV-2 metagenomic sequencing by spiked primer enrichment (MSSPE), library prep protocol.
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SARS-CoV-2 ARTIC sequencing using Illumina, library prep protocol.
Training Materials
A. Metagenomic Sequencing
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Metagenomic sequencing (mNGS): introduction and lab setup.
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mNGS: study design and sample preparation.
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Introduction to Illumina sequencing and data analysis for mNGS using IDseq.
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Library preparation for mNGS.
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Loading the sequencer.
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iSeq loading guide.
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MiSeq loading guide.
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iSeq loading guide.
B. Enrichment/Depletion Methods for Sequencing
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FLASH protocol.
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FLASH.
C. Genomic Epidemiology Learning Materials
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Applied Genomic Epidemiological handbook
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Essential Background Theory for Genomic Epidemiology
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Module 1: The overlapping timescales of pathogen evolution and transmission
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Module 2: From sequences to trees.
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Module 3: Shared terminology for describing phylogenetic trees.
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Module 4: Estimating evolutionary rates (molecular clocks) from sequence data.
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Module 5: Interpreting and working with evolutionary rates.
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Module 6: Using evolutionary rates to infer time trees.
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Module 1: The overlapping timescales of pathogen evolution and transmission
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Seminar Recordings: Foundations of genomic epidemiology
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Mutations, substitutions, and genetic divergence trees.
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Molecular clocks and temporally-resolved trees.
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Phylogeography and trait reconstruction on trees.
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Under the hood with Nextstrain.
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Consensus genome quality control.
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Genomic surveillance data management.
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Phylogenetic nomenclature systems.
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Sampling design in genomic epidemiology.
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Phylodynamic analysis
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Aspen demo + phylogenetic placements
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Antigenic evolution
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Phylogenetic placements versus phylogenetic trees.
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Introduction to genomic epi of TB
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Local cases studies in using genomic epidemiology.
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Genomic epidemiology of mumps virus.
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CZ Gen Epi Tutorial! Aspen feature update: self-serve trees
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Updates to Nextclade quality control metrics.
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Contamination, Coinfection, and Recombination
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Why sequence whole genomes?
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Monkeypox
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Developing a new amplicon-based WGS protocol - Part 1
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Developing a new amplicon-based WGS protocol - Part 2
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Sample size calculations for variant detection and prevalence.
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Mutations, substitutions, and genetic divergence trees.
D. Additional material
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How to make your own SPRI beads.
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Sequencing SARS-CoV-2 for public health laboratories.
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Scaling sequencing.