Pipeline components for real-time virus analysis
Python Shell
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.

README.md

Introduction

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. Documentation is available at nextstrain.org/docs.

Augur

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.

Install

There are currently two parallel but separate versions of augur: original augur (or old augur) and modular augur (or new augur). They can be used at the same time, but we're actively migrating pathogens to use the new, modular augur and eventually old augur will be removed. Currently, both versions live inside this git repository, which can get pretty confusing. These are the files associated with new, modular augur:

augur/
  __init__.py
  align.py
  export.py
  ...
bin/
  augur
setup.py

and these are the files associated with the old augur:

__init__.py
base/
  auspice_export.py
  colorLogging.py
  config.py
  ...
requirements.txt
requirements-locked.txt
scripts/
  beast-to-auspice-jsons-proof-of-principle.py
  json_tree_to_nexus.py
  plot_msa.py

New, modular augur is setup as a standard Python package with several modules that are runnable from the command-line using the augur command. Old augur requires writing Python scripts which import functions and classes from the base/ directory.

Note that old augur requires Python 2.7 while new, modular augur requires Python 3.

To install either version of augur, first clone the git repository:

git clone https://github.com/nextstrain/augur.git
cd augur

Both versions of augur have a number of Python dependencies. The dependencies of old augur are listed in requirements.txt and are best installed via a package manager like conda or pip. You may choose to use requirements-locked.txt if you'd like a fixed set of known-good packages.

pip install -r requirements.txt

The dependencies of new, modular augur are specified in setup.py, which is the standard location for Python packages. You can install modular augur, including the augur command, and all its dependencies using pip3:

pip3 install .

In addition, both versions of augur need working installations of mafft and one of the following tree builders:

Additionally, bacterial builds require a working installation of vcftools.

Dev install

If you're going to be editing augur source code rather than just running augur from command line, it's recommended to install with

pip3 install -e .[dev]

to make module "editable" and install dev dependencies.

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 2014-2018 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.