Related Experiment Video
Updated: Nov 2, 2025

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples
Published on: June 30, 2023
A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive
Miguel Roncoroni1,2, Bert Droesbeke1,2, Ignacio Eguinoa1,2
1Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
Summary:
Many aspects of the global response to the COVID-19 pandemic are enabled by the fast and open publication of SARS-CoV-2 genetic sequence data. The European Nucleotide Archive (ENA) is the European recommended open repository for genetic sequences. In this work, we present a tool for submitting raw sequencing reads of SARS-CoV-2 to 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 bioinformatics knowledge to do bulk sequencing read submissions. The tool is also packed in a Docker container to ease deployment.
Availability And Implementation:
CLI ENA upload tool is available at github.com/usegalaxy-eu/ena-upload-cli (DOI 10.5281/zenodo.4537621); Galaxy ENA upload tool at toolshed.g2.bx.psu.edu/view/iuc/ena_upload/382518f24d6d and github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload (development); and ENA upload Galaxy container at github.com/ELIXIR-Belgium/ena-upload-container (DOI 10.5281/zenodo.4730785).
Related Concept Videos
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Next-generation Sequencing
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
RACE - Rapid Amplification of cDNA Ends
Sanger Sequencing

