https://github.com/cdcgov/tb_molecular_epidemiology

Algorithms for TB molecular epidemiology analysis

https://github.com/cdcgov/tb_molecular_epidemiology

Repository

Algorithms for TB molecular epidemiology analysis

https://github.com/CDCgov/TB_molecular_epidemiology/blob/master/

# TB Molecular Epidemiology
This repository was created for use by CDC programs to collaborate on public health surveillance related projects in support of the CDC Surveillance Strategy.  Github is not hosted by the CDC, but is used by CDC and its partners to share information and collaborate on software.

## Logically Inferred Tuberculosis Transmission (LITT)

LITT is an algorithm that can be used to integrate whole genome sequencing, clinical, and epidemiological data to identify and rank potential sources for tuberculosis cases. More details can be found in our [paper](https://www.frontiersin.org/articles/10.3389/fpubh.2021.667337/full).

## Location And Time To Epi (LATTE)
LATTE identifies all overlaps in space and time from a list of dates that cases (or contacts) were in a particular location, then combines that with infectious periods (IP) to identify and categorize epi or IP epi links.
  
## Public Domain
This repository constitutes a work of the United States Government and is not
subject to domestic copyright protection under 17 USC  105. This repository is in
the public domain within the United States, and copyright and related rights in
the work worldwide are waived through the [CC0 1.0 Universal public domain dedication](https://creativecommons.org/publicdomain/zero/1.0/).
All contributions to this repository will be released under the CC0 dedication. By
submitting a pull request you are agreeing to comply with this waiver of
copyright interest.

## License
The repository utilizes code licensed under the terms of the Apache Software
License and therefore is licensed under ASL v2 or later.

This source code in this repository is free: you can redistribute it and/or modify it under
the terms of the Apache Software License version 2, or (at your option) any
later version.

This source code in this repository 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 Apache Software License for more details.

You should have received a copy of the Apache Software License along with this
program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html

The source code forked from other open source projects will inherit its license.


## Privacy
This repository contains only non-sensitive, publicly available data and
information. All material and community participation is covered by the
Surveillance Platform [Disclaimer](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md)
and [Code of Conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).
For more information about CDC's privacy policy, please visit [http://www.cdc.gov/privacy.html](http://www.cdc.gov/privacy.html).

## Contributing
Anyone is encouraged to contribute to the repository by [forking](https://help.github.com/articles/fork-a-repo)
and submitting a pull request. (If you are new to GitHub, you might start with a
[basic tutorial](https://help.github.com/articles/set-up-git).) By contributing
to this project, you grant a world-wide, royalty-free, perpetual, irrevocable,
non-exclusive, transferable license to all users under the terms of the
[Apache Software License v2](http://www.apache.org/licenses/LICENSE-2.0.html) or
later.

All comments, messages, pull requests, and other submissions received through
CDC including this GitHub page are subject to the [Presidential Records Act](http://www.archives.gov/about/laws/presidential-records.html)
and may be archived. Learn more at [http://www.cdc.gov/other/privacy.html](http://www.cdc.gov/other/privacy.html).

## Records
This repository is not a source of government records, but is a copy to increase
collaboration and collaborative potential. All government records will be
published through the [CDC web site](http://www.cdc.gov).

## Notices
Please refer to [CDC's Template Repository](https://github.com/CDCgov/template)
for more information about [contributing to this repository](https://github.com/CDCgov/template/blob/master/CONTRIBUTING.md),
[public domain notices and disclaimers](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md),
and [code of conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).

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