https://github.com/cdcgov/bmgap
The Bacterial Meningitis Genome Analysis Platform, an analysis pipeline, ExpressJS API, and ReactJS webapp for the analysis and characterization of bacterial meningitis samples
https://github.com/cdcgov/bmgap
Last synced: about 12 hours ago
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The Bacterial Meningitis Genome Analysis Platform, an analysis pipeline, ExpressJS API, and ReactJS webapp for the analysis and characterization of bacterial meningitis samples
- Host: GitHub
- URL: https://github.com/cdcgov/bmgap
- Owner: CDCgov
- License: apache-2.0
- Created: 2020-06-26T18:13:46.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2023-01-04T16:24:30.000Z (over 2 years ago)
- Last Synced: 2025-04-17T00:14:47.899Z (6 days ago)
- Language: Python
- Size: 61.1 MB
- Stars: 7
- Watchers: 6
- Forks: 10
- Open Issues: 34
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Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: code-of-conduct.md
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README
# Bacterial Meningitis Genome Analysis Platform (BMGAP)
**General disclaimer** This repository was created for use by CDC programs to collaborate on public health related projects in support of the [CDC mission](https://www.cdc.gov/about/organization/mission.htm). GitHub is not hosted by the CDC, but is a third party website used by CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise.
## Overview
BMGAP contains an analysis pipeline to identify and characterize bacterial meningitis pathogens using Illumina short-read sequencing, a database and API to store and serve analysis results, and a web-based UI to provide access to the results.
The BMGAP analysis pipeline requires Python 3.6+ as well as a number of dependencies, including BLAST+, MASH, and SPAdes. Data is stored in a MongoDB database, and is served using an ExpressJS-based server. The web UI is implemented using React.
The BMGAP analysis pipeline includes several purpose-built analysis tools, including BMScan, which uses MASH and a custom database to provide species identification for bacterial meningitis pathogens, LocusExtractor, which uses PubMLST references to identify MLSTs for both *Neisseria sp.* and *Haemophilus influenzae*, and PMGA, which identifies and annotates serogrouping/serotyping genes and MLST alleles.
## Access to BMGAP through the OAMD Portal
BMGAP can be accessed online through the OAMD Portal (amdportal-sams.cdc.gov). To request access to BMGAP, please contact the BMGAP team at Shalabh Sharma - [email protected] to register for using the OAMD Portal.
Additional details on the account creation process can be found in the SAMS User Guide: [https://auth.cdc.gov/sams/SAMSUserGuide.pdf?disp=true].
## Public Domain Standard Notice
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 Standard Notice
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 Standard Notice
This repository contains only non-sensitive, publicly available data and
information. All material and community participation is covered by the
[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/other/privacy.html](https://www.cdc.gov/other/privacy.html).
## Contributing Standard Notice
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 may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at [http://www.cdc.gov/other/privacy.html](http://www.cdc.gov/other/privacy.html).
## Records Management Standard Notice
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).
## Additional Standard 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).