A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive

Miguel Roncoroni; Bert Droesbeke; Ignacio Eguinoa; Kim De Ruyck; Flora D'Anna; Dilmurat Yusuf; Björn Grüning; Rolf Backofen; Frederik Coppens

doi:10.1093/bioinformatics/btab421

A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive

Bioinformatics. 2021 Nov 5;37(21):3983-3985. doi: 10.1093/bioinformatics/btab421.

Authors

Miguel Roncoroni^{1

2}, Bert Droesbeke^{1

2}, Ignacio Eguinoa^{1

2}, Kim De Ruyck^{1

2}, Flora D'Anna^{1

2}, Dilmurat Yusuf³, Björn Grüning³, Rolf Backofen³, Frederik Coppens^{1

2}

Affiliations

¹ Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
² VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
³ Department of Computer Science, University of Freiburg, 79110 Freiburg im Breisgau, Baden-Württemberg, Germany.

Abstract

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).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19*
Humans
Nucleotides
Pandemics
SARS-CoV-2
Software*

Substances

Nucleotides