Augur

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens - Published in JOSS (2021)

https://github.com/nextstrain/augur

Science Score: 100.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 6 DOI reference(s) in README and JOSS metadata
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Academic publication links
Links to: joss.theoj.org
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Committers with academic emails
7 of 58 committers (12.1%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
Published in Journal of Open Source Software

Keywords from Contributors

clade sequences dna virus strain sars-cov-2 rna research nextstrain next-generation-sequencing

Scientific Fields

Sociology Social Sciences - 87% confidence

Mathematics Computer Science - 84% confidence

Last synced: 4 months ago · JSON representation ·

Repository

Pipeline components for real-time phylodynamic analysis

Basic Info

Host: GitHub
Owner: nextstrain
License: agpl-3.0
Language: Python
Default Branch: master
Homepage: https://docs.nextstrain.org/projects/augur/
Size: 19.2 MB

Statistics

Stars: 272
Watchers: 30
Forks: 136
Open Issues: 260
Releases: 84

Created over 9 years ago · Last pushed 4 months ago

Metadata Files

Readme Changelog License Citation

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.

Quickstart

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

Documentation

Citation

Huddleston J, Hadfield J, Sibley TR, Lee J, Fay K, Ilcisin M, Harkins E, Bedford T, Neher RA, Hodcroft EB, (2021). Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. Journal of Open Source Software, 6(57), 2906, https://doi.org/10.21105/joss.02906

For other formats, refer to CITATION.cff.

License and copyright

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.

Owner

Name: Nextstrain
Login: nextstrain
Kind: organization

Website: https://nextstrain.org
Twitter: nextstrain
Repositories: 84
Profile: https://github.com/nextstrain

Real-time tracking of pathogen evolution

JOSS Publication

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens

Published

January 07, 2021

DOI

10.21105/joss.02906

Volume 6, Issue 57, Page 2906

Authors

John Huddleston

Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA

James Hadfield