About Nextstrain

Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually-updated view of publicly available data with powerful analytics and visualizations showing pathogen evolution and epidemic spread. Our goal is to aid epidemiological understanding and improve outbreak response.

Resulting data and inferences are available live at the website nextstrain.org.

About Auspice

Definition: Observation by an augur, ie a prophetic sign.

Auspice is an open-source interactive web app for visualizing phylogenomic data. It may be used in tandem with nextstrain's bioinformatics toolkit augur or on its own. Auspice may be used to explore datasets locally or run as a server to share results.

Documentation

The main Nextstrain documentation is available at docs.nextstrain.org. This includes tutorials, how-to guides, and explanations of concepts to help you get started and answer common questions to achieve your goal(s) with Auspice and other Nextstrain tools.

When getting started with Auspice, it may be helpful to read our overview of how Auspice fits together with other Nextstrain tools.

For more detailed technical information how Auspice works and reference guides describing specific Auspice features, check out the Auspice reference-guide documentation at docs.nextstrain.org/projects/auspice.

Quickstart

Installation

See the relevant page on Auspice docs.

Obtain datasets to display

To get up & running, you'll need datasets to visualise. (Please see the nextstrain docs for tutorials on how to run your own analyses.)

If you've installed auspice from npm you may get datasets to display via:

mkdir data
curl http://data.nextstrain.org/zika.json --compressed -o data/zika.json
curl http://data.nextstrain.org/ncov.json --compressed -o data/ncov.json
...

If you've installed auspice from source, we have a helper script to download a number of datasets for testing:

# from the auspice src directory
npm run get-data

Obtain narratives to view locally

This repository contains a number of "test narratives" which serve both to provide examples of the capability of narratives, as well as being used to test functionality and fix bugs. These should work out of the box, assuming you have obtained the necessary datasets via the above script.

If you wish to view the nextstrain-maintained narratives, then this can be done by checking out the nextstrain/narratives github repo and telling auspice to look for narratives there via the --narrativeDir argument.

Run auspice

auspice view --datasetDir data

And view auspice in the browser at localhost:4000

If you are editing source code, running the following command will allow hot-reloading.

auspice develop --datasetDir data

Environment variables

The client looks for some environment variables. All are optional.

[!NOTE] This is an incomplete list. For other variables, search for process.env. in the codebase.

• SKIP_REDUX_CHECKS: Set this to a truthy value to improve dev server responsiveness. Useful when you see a console warning like this:

  ImmutableStateInvariantMiddleware took 200ms, which is more than the warning threshold of 32ms. If your state or actions are very large, you may want to disable the middleware as it might cause too much of a slowdown in development mode.

CLI (Command Line Interface)

Run auspice --help or auspice view --help to see all the available command line options.

Contributor Information

We have received a number of generous offers to contribute developer effort to nextstrain (and auspice) following our work on hCoV-19. We welcome contributions! To get started, please review these resources before submitting a pull request:

• Contributor guide
• Project board with available issues
• Developer docs for Auspice

This project strictly adheres to the Contributor Covenant Code of Conduct.

License and copyright

Copyright 2014-2022 Trevor Bedford and Richard Neher.

Source code to Nextstrain is made available under the terms of the GNU Affero General Public License (AGPL). Nextstrain is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.