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nextstrain
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Description

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.

Documentation

Quickstart

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

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.

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