[](https://github.com/nextstrain/augur/actions/workflows/ci.yaml)
[](https://pypi.org/project/nextstrain-augur/)
[](http://bioconda.github.io/recipes/augur/README.html)
[](https://docs.nextstrain.org/projects/augur/en/stable/)
[](https://www.gnu.org/licenses/agpl-3.0)
[](https://doi.org/10.21105/joss.02906)
## 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](https://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](https://github.com/nextstrain/auspice).
## Quickstart
[Follow instructions to install Augur](https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html).
Try out an analysis of real virus data by [completing the Zika tutorial](https://nextstrain.org/docs/tutorials/zika).
## Documentation
* [Overview of how Augur fits together with other Nextstrain tools](https://docs.nextstrain.org/en/latest/learn/parts.html)
* [Overview of Augur usage](https://docs.nextstrain.org/projects/augur/en/stable/usage/usage.html)
* [Technical documentation for Augur](https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html)
* [Contributor guide](https://github.com/nextstrain/.github/blob/-/CONTRIBUTING.md)
* [Developer docs for Augur](./docs/contribute/DEV_DOCS.md)
* [Changelog](./CHANGES.md)
## 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
## License and copyright
Copyright 2014-2022 Trevor Bedford and Richard Neher.
Source code to Nextstrain is made available under the terms of the [GNU Affero General Public License](LICENSE.txt) (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.
Raw data
{
"_id": null,
"home_page": "https://github.com/nextstrain/augur",
"name": "nextstrain-augur",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.8",
"maintainer_email": null,
"keywords": "nextstrain, molecular epidemiology",
"author": "Nextstrain developers",
"author_email": "trevor@bedford.io, richard.neher@unibas.ch",
"download_url": "https://files.pythonhosted.org/packages/6c/5f/b301bf9b74930e7b81374b5e05004ca31634627c06490e25fb950714f58b/nextstrain_augur-27.0.0.tar.gz",
"platform": null,
"description": "[](https://github.com/nextstrain/augur/actions/workflows/ci.yaml)\n[](https://pypi.org/project/nextstrain-augur/)\n[](http://bioconda.github.io/recipes/augur/README.html)\n[](https://docs.nextstrain.org/projects/augur/en/stable/)\n[](https://www.gnu.org/licenses/agpl-3.0)\n[](https://doi.org/10.21105/joss.02906)\n\n## About Nextstrain\n\nNextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data.\nWe provide a continually-updated view of publicly available data with powerful analytics and visualizations showing pathogen evolution and epidemic spread.\nOur goal is to aid epidemiological understanding and improve outbreak response.\n\nResulting data and inferences are available live at the website [nextstrain.org](https://nextstrain.org).\n\n## About Augur\n\n*Definition: One held to foretell events by omens.*\n\nAugur is the bioinformatics toolkit we use to track evolution from sequence and serological data.\nIt provides a collection of commands which are designed to be composable into larger processing pipelines.\n\nThe output of augur is a series of JSONs that can be used to visualize your results using [Auspice](https://github.com/nextstrain/auspice).\n\n## Quickstart\n\n[Follow instructions to install Augur](https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html).\nTry out an analysis of real virus data by [completing the Zika tutorial](https://nextstrain.org/docs/tutorials/zika).\n\n## Documentation\n\n* [Overview of how Augur fits together with other Nextstrain tools](https://docs.nextstrain.org/en/latest/learn/parts.html)\n* [Overview of Augur usage](https://docs.nextstrain.org/projects/augur/en/stable/usage/usage.html)\n* [Technical documentation for Augur](https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html)\n* [Contributor guide](https://github.com/nextstrain/.github/blob/-/CONTRIBUTING.md)\n* [Developer docs for Augur](./docs/contribute/DEV_DOCS.md)\n* [Changelog](./CHANGES.md)\n\n## Citation\n\nHuddleston 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\n\n## License and copyright\n\nCopyright 2014-2022 Trevor Bedford and Richard Neher.\n\nSource code to Nextstrain is made available under the terms of the [GNU Affero General Public License](LICENSE.txt) (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.\n",
"bugtrack_url": null,
"license": null,
"summary": "A bioinformatics toolkit for phylogenetic analysis",
"version": "27.0.0",
"project_urls": {
"Bug Reports": "https://github.com/nextstrain/augur/issues",
"Change Log": "https://github.com/nextstrain/augur/blob/-/CHANGES.md#next",
"Homepage": "https://github.com/nextstrain/augur",
"Source": "https://github.com/nextstrain/augur"
},
"split_keywords": [
"nextstrain",
" molecular epidemiology"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "8d3ee701fe5320255f5790349375a76ee58860ba9a4ae7153ecdd5d77cb3b35d",
"md5": "a842dc41635becc6ab5471a358c8e0a7",
"sha256": "efc515492cca7ddf77156332272b60b782cccaf5849f6919fb6db670e1304252"
},
"downloads": -1,
"filename": "nextstrain_augur-27.0.0-py3-none-any.whl",
"has_sig": false,
"md5_digest": "a842dc41635becc6ab5471a358c8e0a7",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.8",
"size": 340976,
"upload_time": "2024-12-09T19:22:44",
"upload_time_iso_8601": "2024-12-09T19:22:44.190503Z",
"url": "https://files.pythonhosted.org/packages/8d/3e/e701fe5320255f5790349375a76ee58860ba9a4ae7153ecdd5d77cb3b35d/nextstrain_augur-27.0.0-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "6c5fb301bf9b74930e7b81374b5e05004ca31634627c06490e25fb950714f58b",
"md5": "5fef91d7b4a81deae1bf28753d0462e7",
"sha256": "4b0e9b83e84ea8a8a8513535498e50d6540ee3ae4c028a2836787407594f666a"
},
"downloads": -1,
"filename": "nextstrain_augur-27.0.0.tar.gz",
"has_sig": false,
"md5_digest": "5fef91d7b4a81deae1bf28753d0462e7",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.8",
"size": 323753,
"upload_time": "2024-12-09T19:22:46",
"upload_time_iso_8601": "2024-12-09T19:22:46.563798Z",
"url": "https://files.pythonhosted.org/packages/6c/5f/b301bf9b74930e7b81374b5e05004ca31634627c06490e25fb950714f58b/nextstrain_augur-27.0.0.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-12-09 19:22:46",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "nextstrain",
"github_project": "augur",
"travis_ci": false,
"coveralls": true,
"github_actions": true,
"lcname": "nextstrain-augur"
}
JSON
