In this workshop, we will begin by stepping through the available options to submit SARS-CoV-2 data to the European Nucleotide Archive using a series of example data and files we’ve prepared for you. For a complete submissions guide, please see here.
The goal of this workshop is to submit 3 samples to an example project, along with raw read data and sequences associated with each sample. We will do this using a number of different submission options.
Metadata Model Guide¶
Before submitting any data, it is important to understand the structure of our metadata model. This model is used, not only for SARS-CoV-2 data, but data from across the tree of life. In this short video, I will touch on the importance of each element of the model and what data/metadata each object holds.
programmatic: most suitable for high-throughput, frequent submissions and automated systems
interactive: most suitable for infrequent submission, or those more comfortable with spreadsheets
drag-and-drop uploader: most suitable for once-off submission of small-to-meduim scale datasets
We will use the test servers for this workshop. These service URLs begin with
www. Submissions to this service are removed nightly.
Before we begin, please download the example data here and unzip it. For this tutorial, you will need:
a means to view/edit spreadsheets in Microsoft Excel format and a text editor, ideally something with syntax highlighting for XML formatted files.
a command line utility with cURL installed.
basic command line skills.
a Webin account. If you don’t already have one, please register here.
an installation of Webin-CLI, our command line interface for the submission of data files . This requires Java 1.8 or higher.
Now, let’s get started with registering a study.