Skip to content
/ seqsender Public
generated from CDCgov/template

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

cdcgov.github.io/seqsender/

License

Apache-2.0 license
35 stars 14 forks Branches Tags Activity
Star
Notifications You must be signed in to change notification settings

CDCgov/seqsender

BranchesTags

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

171 Commits
.github
.github
 
 
config
config
 
 
docs
docs
 
 
inst
inst
 
 
man/figures
man/figures
 
 
shiny
shiny
 
 
test_data
test_data
 
 
.dockerignore
.dockerignore
 
 
.gitattributes
.gitattributes
 
 
.gitignore
.gitignore
 
 
DESCRIPTION
DESCRIPTION
 
 
Dockerfile
Dockerfile
 
 
LICENSE
LICENSE
 
 
NEWS.md
NEWS.md
 
 
README.Rmd
README.Rmd
 
 
README.md
README.md
 
 
_pkgdown.yml
_pkgdown.yml
 
 
argument_handler.py
argument_handler.py
 
 
biosample_sra_handler.py
biosample_sra_handler.py
 
 
docker-compose.yaml
docker-compose.yaml
 
 
env.yaml
env.yaml
 
 
file_handler.py
file_handler.py
 
 
genbank_handler.py
genbank_handler.py
 
 
gisaid_handler.py
gisaid_handler.py
 
 
mypy.ini
mypy.ini
 
 
ncbi_handler.py
ncbi_handler.py
 
 
seqsender-kickoff
seqsender-kickoff
 
 
seqsender.py
seqsender.py
 
 
settings.py
settings.py
 
 
setup.py
setup.py
 
 
tools.py
tools.py
 
 
upload_log.py
upload_log.py
 
 

Repository files navigation

SeqSender

Public Database Submission Pipeline

Docker pulls Docker image size GitHub last commit

Beta Version: 1.3.3. 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.

Documentation

Overview

seqsender is a Python program that is developed to automate the process of generating necessary submission files and batch uploading them to

About

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

cdcgov.github.io/seqsender/

Topics

bioinformatics-pipeline genbank ncbi-submission ncbi-genbank cdc sra ncbi-sra ncbi-biosamples gisaid gisaid-uploader biosample gisaid-format gisaid-upload seqsender ncird ncird-id cdc-influenza-division

Resources

Readme

License

Apache-2.0 license
Activity
Custom properties

Stars

35 stars

Watchers

3 watching

Forks

14 forks
Report repository

Releases 12

V1.3.3 Latest
Apr 7, 2025
+ 11 releases

Packages

 
 
 

Contributors 5

Languages