The ENA Upload Tool assists in submitting raw sequencing reads of SARS-CoV-2 to the European Nucleotide Archive (ENA). The tool features a single-step submission process, a graphical user interface, tabular-formatted metadata and the possibility to remove human reads prior to submission.

A Galaxy wrap of the tool allows users with little or no bioinformatic knowledge to do bulk sequencing read submissions. The tool is also packed in a Docker container to ease deployment. Available formats: Command-line-interface ENA Upload Tool, Galaxy ENA Upload Tool, ENA Upload Galaxy container.


The tool was developed by ELIXIR Belgium in 2020, further developments (e.g. for the submission of consensus sequences) are ongoing. Extensive documentation is available in our RDM Guide, the manuscript can be read here.