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About

  • Introduction
  • What is Nextstrain?
  • Parts of a whole
  • 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
    • 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
      • Migrate from S3
    • Nextstrain Community
    • Public URLs
    • SARS-CoV-2 datasets
    • Downloading data
  • Communicating scientific insights
    • Communicating Results Using Narratives
    • Converting a narrative to PDF
  • Contributing

Reference

  • Glossary
  • Data formats
  • Augur
  • Auspice
  • Nextstrain CLI
  • Nextclade CLI
  • Nextalign CLI
  • FAQ
  • Style guide
Nextstrain
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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
  • 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 5b5f71fc.

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 2022, Trevor Bedford and Richard Neher
Revision 5b5f71fc.

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