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Table of contents

  • Nextstrain Documentation
  • Learn
    • About Nextstrain
    • Interpreting Nextstrain
      • How to interpret the phylogenetic trees
      • Interacting with Nextstrain’s phylogeographic visualisations
      • Interpreting the Map
    • Pathogens
      • Coronavirus
        • COVID-19 Frequently Asked Questions
        • SARS-CoV-2
        • Technical FAQs
        • Human CoV
  • Tutorials
    • Quickstart
    • SARS-CoV-2
      • A Getting Started Guide to the Genomic Epidemiology of SARS-CoV-2
      • Setup and installation
      • Preparing your data
      • Orientation: so, what does Nextstrain do?
      • Overview of this repository (i.e., what do these files do?)
      • Running the analysis
      • Customizing analysis
      • Customizing your Auspice visualization
      • Clade Naming & Definitions
      • Visualizing and sharing results
      • Guidance for interpretation
      • Nextstrain Narratives
    • Zika Tutorial
    • Zika tutorial – fasta input
    • MTb tutorials using vcf data
    • Writing a Narrative
  • How-to Guides
    • Installing Nextstrain
      • Local Installation
      • Nextstrain CLI installation
      • Augur Installation
      • Auspice Installation
      • Help! I’m using Windows
    • Running Bioinformatic Analyses
      • Manually Labeling Clades on a Nextstrain Tree
      • Augur and snakemake
      • Finding a translate and align reference file
      • Importing BEAST MCC trees into augur
      • Adding Custom Trait Colors
      • Adding Custom Lat-Long Data
      • Using VCF Input
      • Using Fasta Input
      • Inferring Sequence Traits (like Drug Resistance)
      • Examples of Augur in the wild
    • Sharing Analyses through Nextstrain
      • Scalable Sharing with Nextstrain Groups
      • Community Sharing of Results Via GitHub
      • Fetch datasets & narratives accessible via a public URL
      • Download data
    • Communicating scientific insights
      • Communicating Results Using Narratives
      • Converting a narrative to PDF
    • Contributing to Nextstrain
      • Nextstrain Github Contributing Guide
      • Contributing to Documentation
      • Contribute to Nextstrain CLI
      • Contribute to Augur
      • Contribute to Auspice
  • Reference Guides
    • Data formats of Nextstrain
      • Data Formats Used by Nextstrain
    • Augur: A bioinformatics toolkit for phylogenetic analysis
    • Auspice: An Open-source Interactive Tool for Visualising Phylogenomic Data
    • Nextstrain command-line interface (CLI)
Nextstrain
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  • SARS-CoV-2
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SARS-CoV-2¶

Table of contents

  • A Getting Started Guide to the Genomic Epidemiology of SARS-CoV-2
  • Setup and installation
  • Preparing your data
  • Orientation: so, what does Nextstrain do?
  • Overview of this repository (i.e., what do these files do?)
  • Running the analysis
  • Customizing analysis
  • Customizing your Auspice visualization
  • Clade Naming & Definitions
  • Visualizing and sharing results
  • Guidance for interpretation
  • Nextstrain Narratives
Next Previous

Revision a2a977e4.

Hadfield et al., Nextstrain: real-time tracking of pathogen evolution , Bioinformatics (2018)

Nextstrain is built by

Trevor Bedford , Richard Neher , James Hadfield , Emma Hodcroft , Thomas Sibley , John Huddleston , Jover Lee , Kairsten Fay , Sidney Bell , Colin Megill , Barney Potter , Pavel Sagulenko , Charlton Callender , Misja Ilcisin , Louise Moncla , Allison Black , Anderson Brito , Nate Grubaugh
All source code is freely available under the terms of the GNU Affero General Public License. Screenshots may be used under a CC-BY-4.0 license and attribution to nextstrain.org must be provided.
This work is made possible by the open sharing of genetic data by research groups from all over the world. We gratefully acknowledge their contributions. Special thanks to Kristian Andersen, David Blazes, Peter Bogner, Matt Cotten, Ana Crisan, Gytis Dudas, Vivien Dugan, Karl Erlandson, Nuno Faria, Jennifer Gardy, Becky Kondor, Dylan George, Ian Goodfellow, Betz Halloran, Christian Happi, Jeff Joy, Paul Kellam, Philippe Lemey, Nick Loman, Sebastian Maurer-Stroh, Oliver Pybus, Andrew Rambaut, Colin Russell, Pardis Sabeti, Katherine Siddle, Kristof Theys, Dave Wentworth, Shirlee Wohl and Nathan Yozwiak for comments, suggestions and data sharing.
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© Copyright 2020, Trevor Bedford and Richard Neher
Revision a2a977e4.

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