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Nextstrain CLI
version 10.2.0
  • Introduction
  • Installation
  • Upgrading
  • AWS Batch

Commands

  • nextstrain run
  • nextstrain build
  • nextstrain view
  • nextstrain deploy
  • nextstrain remote
  • nextstrain remote list
  • nextstrain remote download
  • nextstrain remote upload
  • nextstrain remote delete
  • nextstrain shell
  • nextstrain update
  • nextstrain setup
  • nextstrain check-setup
  • nextstrain login
  • nextstrain logout
  • nextstrain whoami
  • nextstrain authorization
  • nextstrain version

Remotes

  • nextstrain.org
  • Amazon S3

Runtimes

  • Overview
  • Docker
  • Conda
  • Singularity
  • AWS Batch
  • Ambient

Configuration

  • Config file
  • Paths

Development

  • Glossary
Nextstrain CLI
  • Home
  • Nextstrain CLI

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 2018–2025, Trevor Bedford and Richard Neher

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