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  • Introduction
  • What is Nextstrain?
  • Parts of a whole
  • Augur → Auspice
  • Interpreting analyses
    • Phylogenetic trees
    • Phylogeographic map
    • Interaction
  • Pathogens
  • Nextstrain Groups

Tutorials

  • Installing
  • Running a pathogen workflow
  • Creating a pathogen workflow
  • Exploring SARS-CoV-2 evolution
  • Creating a bacterial pathogen workflow
  • Writing a narrative
  • Analyzing genomes with Nextclade

How-to Guides

  • Bioinformatics
    • Manually Labeling Clades on a Nextstrain Tree
    • Augur and snakemake
    • Missing sequence data (gaps, indels, ambiguity)
    • 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
    • Nextstrain Groups
      • Customize your page
    • Nextstrain Community
    • Public URLs
    • SARS-CoV-2 datasets
    • Downloading data
  • Communicating scientific insights
    • Communicating Results Using Narratives
    • Converting a narrative to PDF
  • Managing an installation
  • Contributing

Components

  • Augur
  • Auspice
  • Nextstrain CLI
  • Nextclade CLI
  • Nextalign CLI
  • nextstrain.org

Reference

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  • Data files
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  • Snakemake style guide
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Running Bioinformatic Analyses

How-to guides for performing bioinformatic anaylses with Nextstrain.

Table of contents

  • Manually Labeling Clades on a Nextstrain Tree
  • Augur and snakemake
  • Missing sequence data (gaps, indels, ambiguity)
  • 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
Previous Next

Revision 568a6754.

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

The core Nextstrain team is

Trevor Bedford , Richard Neher , Ivan Aksamentov , 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 2023, Trevor Bedford and Richard Neher
Revision 568a6754.

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