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.

We have received a number of generous offers to contribute developer effort to nextstrain (and auspice) following our work on SARS-CoV-2. We are flattered and would welcome contributions! Please see the contributing documentation for more details. A list of potential issues is being actively maintained at https://github.com/orgs/nextstrain/projects/5

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 as a server to share results.

Please see nextstrain.github.io/auspice for auspice documentation.

npm install --global auspice

See here for full instructions, including how to install from source.

In order to get up & running you'll need to have some datasets to visualise. Please see the nextstrain docs for tutorials on how to do this. For the purposes of getting started, you can download the current zika dataset via:

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

And then run auspice via:

auspice view --datasetDir data

This will allow you to run auspice locally (i.e. from your computer) and view the dataset which is behind nextstrain.org/zika.

To download all the datasets at once, the following helper command will populate the /data folder.

  npm run get-data

Run auspice --help or visit nextstrain.github.io/auspice for more information.

Auspice is developed via GitHub and issues are very welcome. Alternatively, email us with any questions or comments you may have. If you are interested in submitting a pull request please use eslint as much as possible -- thanks!

New versions are released via the ./releaseNewVersion.sh script from an up-to-date master branch. It will prompt you for the version number increase, push changes to the release branch and, as long as Travis-CI is successful then a new version will be automatically published to npm.

Please see docs-src/README for how the auspice documentation site is built.

Note that currently the documentation must be rebuilt & pushed to GitHub after a new version is released in order for the changelog to correctly appear at nextstrain.github.io/auspice/releases/changelog.

Copyright 2014-2019 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.