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.
Definition: One held to foretell events by omens.
Augur is the bioinformatic processing pipeline to track evolution from sequence and serological data. Documentation for augur is available at nextstrain.org/docs/bioinformatics-pipeline.
To install augur, clone the git repository and its 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 are best installed via a package manager like conda or pip.
pip install -r requirements.txt
Augur is written in Python 2.7 and requires Python 2.7 to run. Your version of Python can be confirmed by running
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 -> raxmlHPCbecause
augurexpects an excutable named
- OPTIONAL: FastTree
- OPTIONAL: IQ-TREE
Each virus build consists of a
process.py file. Currently supported builds are listed in the builds directory.
License and copyright
Copyright 2014-2018 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.