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 hCoV-19. 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
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.
Install auspice for use as a global command. This requires nodejs 10+. We recommend using a conda environment, but this is not the only way.
conda create --name auspice nodejs=10
conda activate auspiceInstall auspice from npm:
npm install --global auspiceOr install auspice from source:
git clone https://github.com/nextstrain/auspice.git
cd auspice
npm install --global .(See here for more installation methods & help).
In order 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 helper scripts to make all the datasets & narratives you see on nextstrain.org available locally:
# from the auspice src directory
npm run get-data
npm run get-narrativesauspice view --datasetDir dataAnd 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
Run auspice --help (or auspice view --help) to see all the available command line options.
Full documentation may be found at: nextstrain.github.io/auspice.
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.