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.
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.
- Overview of how Augur fits together with other Nextstrain tools
- Overview of Augur usage
- Technical documentation for Augur
- Contributor guide
- Project board with available issues
- Developer docs for Augur
Augur is written in Python 3 and requires at least Python 3.6.
To install, run:
pip install nextstrain-augur[full]Augur uses some common external bioinformatics programs which you'll need to install to have a fully functioning toolkit:
-
augur alignrequires mafft -
augur treerequires at least one of: -
Bacterial data (or any VCF usage) requires vcftools
On macOS, you can install these external programs using Homebrew with:
brew tap brewsci/bio
brew install mafft iqtree raxml fasttree vcftoolsOn Debian/Ubuntu, you can install them via:
sudo apt install mafft iqtree raxml fasttree vcftoolsFor more extensive installation instructions, please see the technical docs
All of Augur's commands are accessed through the augur program.
For example, to infer ancestral sequences from a tree, you'd run augur ancestral.
If you've installed the nextstrain-augur package, you can just run augur.
Otherwise, you can run ./bin/augur from a copy of the source code.
usage: augur [-h] {parse,filter,mask,align,tree,refine,ancestral,translate,clades,traits,sequence-traits,titers,export,validate,version} ...
Augur: A bioinformatics toolkit for phylogenetic analysis.
positional arguments:
{parse,filter,mask,align,tree,refine,ancestral,translate,clades,traits,sequence-traits,titers,export,validate,version}
parse Parse delimited fields from FASTA sequence names into
a TSV and FASTA file.
filter Filter and subsample a sequence set.
mask Mask specified sites from a VCF file.
align Align multiple sequences from FASTA or VCF.
tree Build a tree using a variety of methods.
refine Refine an initial tree using sequence metadata.
ancestral Infer ancestral sequences based on a tree.
translate Translate gene regions from nucleotides to amino
acids.
clades Assign clades to nodes in a tree based on amino-acid
or nucleotide signatures.
traits Infer ancestral traits based on a tree.
sequence-traits Annotate sequences based on amino-acid or nucleotide
signatures.
titers Annotate a tree with actual and inferred titer
measurements.
export Export JSON files suitable for visualization with
auspice.
validate Validate a set of JSON files intended for
visualization in auspice.
version Print the version of augur.
optional arguments:
-h, --help show this help message and exit
For more information on a specific command, you can run it with the --help option, for example, augur tree --help.
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.