About this tutorial

Fast and open access to different data types (societal, molecular, epidemiological, among others) was key to the swift development and deployment of, for example, preventative measures, tests, vaccines, and treatments for COVID-19. The pandemic has thus further highlighted how important making data open and FAIR (Findable, Accessible, Interoperable, Reusable) is in facilitating research efforts. Many SARS-CoV-2 genome sequences have been made openly available in international databases, such as the Global Initiative on Sharing Avian Influenza Data (GISAID), and the European Nucleotide Archive (ENA).

The aim of this tutorial is to assist researchers in submitting SARS-CoV-2 sequence data to ENA. This should ultimately lead to an increased availability of open data, including ‘raw’ sequence data, thus faciliting greater reproducibility as well as providing more opportunity for reusing the data to address new scientific questions.

Overview

This tutorial is separated into tabs to aid users in moving through the tutorial. If you are unfamiliar with ENA, we recommend reading the Terminology and Metadata tab before commencing with the tutorial.

Multiple routes of submission are possible with ENA. We describe two complete routes that can be used for submission. Some preparatory steps are common to both routes. These steps are described in the Preparations for Submissions tab. We explain how to determine which of the routes is most likely to work best for you in the Select Submission Route tab. The Submission Route 1 and Submission Route 2 tabs explain different routes to completing submissions to ENA.

Information about where to get further guidance is given in the Get Help tab. For answers to frequently asked questions (FAQs) regarding submissions, please see the FAQs tab.

Learning outcomes

By the end of this tutorial you will:

• Understand the terminology used by ENA (and other similar databases).

• Know how to properly describe and format SARS-CoV-2 data for submission into ENA.

• Know how to complete a submission into ENA.

• Know where to get help for future submissions (whether for SARS-CoV-2, or something else) to ENA.

Prerequisites

No specific knowledge is needed before starting this tutorial.

References used for this tutorial

Multiple sources of information were used to build this tutorial. Links to the reference material are listed below:

• Teaching module on submission to data repositories, by NBIS Sweden.

• SARS-CoV-2 submission workshop, by ENA.

• Additional documentation about submission of SARS-CoV-2 data to ENA, by ENA.

• SARS-CoV-2 ENA submission workflow and guidance for structuring and releasing metadata V.2., by Alikhan, N. -F., Timme, R. E., and Griffiths, E.

• General guide on ENA data submission, by ENA.

• Research Data Management (RDM) Guide, by ELIXIR-Belgium.

• GitHub repository for ELIXIR-Belgium ENA upload container.

• GitHub repository for MultiSub command line submission tool.