slavkoder / auspice

Web app for visualizing pathogen evolution

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 as a server to share results.

Documentation

• Overview of how Auspice fits together with other Nextstrain tools
• Auspice documentation

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 see these resources:

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

Quickstart

Installation

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 auspice

Install auspice from npm:

npm install --global auspice

Or install auspice from source:

git clone https://github.com/nextstrain/auspice.git
cd auspice
npm install --global .

(See here for more installation methods & help).

Obtain datasets to display:

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-narratives

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

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.

License and copyright

Copyright 2014-2020 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.