SeqSender

Public Database Submission Pipeline

Beta Version: 1.3.93. 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.

Documentation

Overview

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.

Available Versions

SeqSender can be installed a couple of different ways. All SeqSender versions are updated when a new GitHub version is released. SeqSender can be setup by directly cloning from GitHub or the docker image can be downloaded from the GitHub Container Repository or DockerHub.

Contacts

Role	Contact
Creator	Dakota Howard, Reina Chau
Maintainer	Dakota Howard
Back-Up	Reina Chau, Brian Lee

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
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the CC0 1.0 Universal public domain
dedication. All
contributions to this repository will be released under the CC0
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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
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This source code in this repository is distributed in the hope that it
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Additional Standard Notices

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Repository for more information
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