Submission of SARS-CoV-2 sequence data to ENA using Galaxy
Channel: ELIXIR Belgium
Date: 2021-01-04

This video gives a walkthrough on how to upload raw sequences for SARS-COV-2 along with its metadata to European Nucleotide Archive (ENA) using our Galaxy tool. It also includes how to remove human reads from the viral data, so no sensitive data is shared. 

All details can also be found at our website https://rdm.elixir-belgium.org/covid-19. 

Links discussed in this video:
* Get docker
  https://docs.docker.com/get-docker/

* ENA-Register for Webin ID
  https://www.ebi.ac.uk/ena/submit/sra/#registration

* ENA-submission portal public server
  https://www.ebi.ac.uk/ena/submit/webin

* ENA-submission portal test server
  https://wwwdev.ebi.ac.uk/ena/submit/webin

* Short introduction to Galaxy
  https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-short/tutorial.html

* Metadata template for viral sequence reads submission to ENA
  https://drive.google.com/file/d/1dulhBEfRO56ldCnuaIhjjtNbJDxQ5K1v/view?usp=sharing


Chapters in this video:
00:00 Intro
00:40 Running the container
02:34 Using the Galaxy container
03:27 Managing credentials
04:20 Upload data
05:29 Remove human reads
07:09 Submitting reads to ENA
12:01 Checking the submission
13:14 Thank you

Special thanks to:
FWO - EWI - EOSC Life - Elixir Converge - VIB - EBI - Covid-19 dataportal