Public Database Submission Pipeline
Beta Version: 1.2.3. This pipeline is currently in Beta testing, and issues could appear during submission. Please use it at your own risk. Feedback and suggestions are welcome!
General Disclaimer: This repository was created for use by CDC programs to collaborate on public health related projects in support of the CDC mission. 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.
seqsender is a Python program that is developed to automate the
process of generating necessary submission files and batch uploading
them to NCBI archives (such as BioSample, SRA, and
Genbank) and GISAID databases (e.g. EpiFlu,
EpiCoV, EpiPox, EpiArbo). Presently, the pipeline is capable
of uploading Influenza A Virus (FLU), SARS-COV-2 (COV),
Monkeypox (POX), Arbovirus (ARBO), and a wide variety of other
organisms. If you’d like to have seqsender support your virus create a
issue.
| Role | Contact |
|---|---|
| Creator | Dakota Howard, Reina Chau |
| Maintainer | Dakota Howard |
| Back-Up | Reina Chau, Brian Lee |
Dakota Howard and Reina Chau for majority of the code base with input and testing from colleagues.
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. 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.
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.
This repository contains only non-sensitive, publicly available data and information. All material and community participation is covered by the Disclaimer and Code of Conduct. For more information about CDC’s privacy policy, please visit http://www.cdc.gov/other/privacy.html.
Anyone is encouraged to contribute to the repository by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) 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 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.
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.
Please refer to CDC’s Template Repository for more information about contributing to this repository, public domain notices and disclaimers, and code of conduct.