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SARS-CoV-2 Workflow
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Table of contents

  • Getting started with analysis
    • 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
  • Getting started with visualization & interpretation
    • Visualizing and sharing results
    • Guidance for interpretation
    • Nextstrain Narratives
  • Guides
    • Terra Workflow
  • Reference material
    • Running an analysis starting from multiple inputs
    • Overview of remote nCoV files (intermediate build assets)
    • Configuration parameters for Nextstrain SARS-CoV-2 workflow
    • Standard Nextstrain metadata fields
    • Clade Naming & Definitions
    • Data Submitter’s FAQ
    • Change Log
  • Video tutorial walkthrough
  • Stuck? Ask us on the discussion board. We're happy to help!
SARS-CoV-2 Workflow
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  • SARS-CoV-2 Workflow

Revision 82485263.

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 , Ivan Aksamentov , Jover Lee , Kairsten Fay , Moira Zuber , Eli Harkins , Misja Ilcisin , Cassia Wagner , Louise Moncla , Allison Black , Sidney Bell , Miguel Parades , Colin Megill , Barney Potter , Pavel Sagulenko , Charlton Callender
All source code for Nextstrain is freely available under the terms of an open-source license, typically AGPL-3.0 or MIT. Refer to specific projects for details. 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, Josh Batson, David Blazes, Jesse Bloom, Peter Bogner, Anderson Brito, Matt Cotten, Ana Crisan, Tulio de Oliveira, Gytis Dudas, Vivien Dugan, Karl Erlandson, Nuno Faria, Jennifer Gardy, Nate Grubaugh, Becky Kondor, Dylan George, Ian Goodfellow, Betz Halloran, Christian Happi, Jeff Joy, Paul Kellam, Philippe Lemey, Nick Loman, Duncan MacCannell, Erick Matsen, Sebastian Maurer-Stroh, Placide Mbala, Danny Park, Oliver Pybus, Andrew Rambaut, Colin Russell, Pardis Sabeti, Katherine Siddle, Kristof Theys, Dave Wentworth, Shirlee Wohl and Cecile Viboud for comments, suggestions and data sharing.
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© Copyright 2014–2022 Trevor Bedford and Richard Neher
Revision 82485263.

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