General Guide on ENA Data Submission

Welcome to the general guide for the European Nucleotide Archive submission. Please take a moment to view this introduction and consider the options available to you before you begin your submission.

ENA allows submissions via three routes, each of which is appropriate for a different set of submission types. You may be required to use more than one in the process of submitting your data:

  • Interactive Submissions are completed by either filling out web forms directly in your browser or alternatively downloading spreadsheets that can be completed off-line and uploaded to ENA. This is often the most accessible submission route.
  • Command Line Submissions use our bespoke Webin-CLI program. This validates your submissions entirely before you complete them, allowing you maximum control of the process.
  • Programmatic Submissions are completed by preparing your submissions as XML documents and either sending them to ENA using a program such as cURL or using the Webin Submissions Portal.

The table below outlines what can be submitted through each submission route. It is also recommended that you familiarise yourself with our metadata model.

  Interactive Webin-CLI Programmatic
Study Y N Y
Sample Y N Y
Read data Y Y* Y
Genome Assembly N Y N
Transcriptome Assembly N Y N
Template Sequence Y Y N
Other Analyses N N Y

* Webin-CLI accepts read submission in FASTQ, BAM, or CRAM format. For other formats use either of the other submission routes.

Before submitting to ENA it is important to familiarise yourself with the different options available for data submission. This general guide will get you started in understanding how data can be submitted to ENA and how to keep track of the progress of your submission.