Skip to content
Permalink
master
Switch branches/tags
Go to file
 
 
Cannot retrieve contributors at this time

Welcome to Nextstrain's documentation!

Nextstrain is a project to harness the scientific and public health potential of pathogen genome data. It's made up of many different parts that all work together. Through our website, nextstrain.org, we provide a continually-updated view of publicly available data with powerful analyses and visualizations showing pathogen evolution and epidemic spread. Through our open-source software tools, we aim to help you analyze and visualize your own data in the same way. Our goal is to aid epidemiological understanding and improve outbreak response.

Our intent for this documentation site is to cover all parts of Nextstrain, from viewing the website to producing your own analyses to contributing to Nextstrain's development.

Hint

If you're new to Nextstrain, start with :doc:`/learn/about`.

If you're interested in how to interpret what you see on nextstrain.org, start with :doc:`/learn/interpret/index`.

If you're ready to go beyond viewing the website (or just plain curious!), start with :doc:`/learn/parts`.

If you have questions, need help, or simply want to say hi, post to our discussion forum where the Nextstrain team and other Nextstrain users provide assistance. For private inquiries, email the Nextstrain team.

.. toctree::
    :maxdepth: 1
    :titlesonly:
    :caption: About
    :hidden:

    Introduction <self>
    learn/about
    learn/parts
    learn/interpret/index
    Pathogens <learn/pathogens/index>
    learn/groups/index

.. toctree::
    :maxdepth: 1
    :titlesonly:
    :caption: Tutorials
    :hidden:

    Installing <install>
    tutorials/running-a-workflow
    tutorials/creating-a-workflow
    Exploring SARS-CoV-2 evolution <https://docs.nextstrain.org/projects/ncov/en/latest/index.html>
    tutorials/creating-a-bacterial-pathogen-workflow
    Writing a narrative <tutorials/narratives-how-to-write>
    Analyzing genomes with Nextclade <https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextclade-web.html>

.. toctree::
    :maxdepth: 1
    :titlesonly:
    :caption: How-to Guides
    :hidden:

    Bioinformatics <guides/bioinformatics/index>
    Sharing analyses <guides/share/index>
    Communicating scientific insights <guides/communicate/index>
    Contributing <guides/contribute/index>

.. toctree::
    :maxdepth: 1
    :titlesonly:
    :caption: Reference
    :hidden:

    reference/glossary
    reference/data-formats
    Augur <https://docs.nextstrain.org/projects/augur/en/stable/index.html>
    Auspice <https://docs.nextstrain.org/projects/auspice/en/stable/>
    Nextstrain CLI <https://docs.nextstrain.org/projects/cli/en/stable/>
    Nextclade CLI <https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextclade-cli.html>
    Nextalign CLI <https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextalign-cli.html>
    reference/style