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SARS-CoV-2 Workflow

Tutorials

  • Introduction
  • Setup and installation
  • Run using example data
  • Run using custom data
  • Run using a genomic surveillance configuration
  • Next steps
  • Video tutorial walkthrough

Visualization & Interpretation

  • Visualizing and sharing results
  • Guidance for interpretation
  • Nextstrain Narratives

Guides

  • Update the workflow
  • Data preparation guide
    • Prepare your own local data
    • Curate data from GISAID search and downloads
    • Curate data from the full GISAID database
  • Workflow config file guide
  • Customizing visualization
  • Run the workflow on Terra

Reference

  • Nextstrain overview
  • Files overview
  • Workflow config file reference
  • Remote inputs
  • Standard metadata fields
  • Clade Naming & Definitions
  • Data Submitter’s FAQ
  • Troubleshoot common issues
  • Change Log
  • Glossary
  • Stuck? Ask us on the discussion board. We're happy to help!
SARS-CoV-2 Workflow
  • Home
  • SARS-CoV-2 Workflow

Index

A | C | D | N | S

A

  • analysis directory
  • Auspice config file

C

  • config file
  • customization file

D

  • default files

N

  • ncov workflow

S

  • Snakemake

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

The core Nextstrain team is

Trevor Bedford , Richard Neher , Ivan Aksamentov , John SJ Anderson , Kim Andrews , Jennifer Chang , James Hadfield , Emma Hodcroft , John Huddleston , Jover Lee , Victor Lin , Cornelius Roemer , Thomas Sibley

Please see the team page for more details.


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 2014–2024 Trevor Bedford and Richard Neher

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