Pipeline components for real-time phylodynamic analysis
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Build Status PyPI version install with bioconda Documentation Status License: AGPL v3 DOI

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 Augur

Definition: One held to foretell events by omens.

Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data. It provides a collection of commands which are designed to be composable into larger processing pipelines.

The output of augur is a series of JSONs that can be used to visualize your results using Auspice.


Follow instructions to install Augur. Try out an analysis of real virus data by completing the Zika tutorial.



Huddleston J, Hadfield J, Sibley TR, Lee J, Fay K, Ilcisin M, Harkins E, Bedford T, Neher RA, Hodcroft EB, (2021). Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. Journal of Open Source Software, 6(57), 2906, https://doi.org/10.21105/joss.02906

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.