Pipeline components for real-time phylodynamic analysis

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.

Documentation

• 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

Quickstart

Installation

Augur is written in Python 3 and requires at least Python 3.4.

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 align requires mafft

• augur tree requires at least one of:

  • IQ-TREE (used by default)
  • RAxML (optional alternative)
  • FastTree (optional alternative)

• 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 vcftools

On Debian/Ubuntu, you can install them via:

sudo apt install mafft iqtree raxml fasttree vcftools

For more extensive installation instructions, please see the technical docs

Basic Usage

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.

License and copyright

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.