Pipeline components for real-time virus analysis


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.

Nextstrain is comprised of three primary components:

  • fauna: database and IO scripts for sequence and serological data
  • augur: informatic pipelines to conduct inferences from raw data
  • auspice: web app to visualize resulting inferences

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


Definition: One held to foretell events by omens.

Augur is the informatic processing pipeline to track evolution from sequence and serological data. It is broken into two parts, termed prepare and process, which result in output JSONs for Auspice.



To install augur, clone the git repository and the submodules git clone https://github.com/nextstrain/augur.git cd augur git submodule update --init Augur has a number of python dependencies that are listed in requirements.txt and best installed via a package manager like conda or pip. pip install -r requirements.txt In addition, augur needs working installations of mafft and one of the following tree builders * DEFAULT: RAxML. You'll probably need to create a symlink raxml -> raxmlHPC because augur expects an excutable named raxml * OPTIONAL: FastTree * OPTIONAL: IQ-TREE


Docs are available for prepare, process and Auspice JSON format.

Virus builds

Each virus build consists of a prepare.py and process.py file. Currently supported builds are listed in the builds directory.

License and copyright

Copyright 2014-2017 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.