Awesome

<em>Public Database Submission Pipeline</em>

Beta Version: 1.2.5. 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!

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Documentation

Overview

seqsender is a Python program that is developed to automate the process of generating necessary submission files and batch uploading them to <ins>NCBI archives</ins> (such as BioSample, SRA, and Genbank) and <ins>GISAID databases</ins> (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.

Contacts

Code Attributions

Dakota Howard and Reina Chau for majority of the code base with input and testing from colleagues.

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. 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.

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

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Additional Standard Notices

Please refer to CDC’s Template Repository for more information about contributing to this repository, public domain notices and disclaimers, and code of conduct.