Analysis and mobilisation of publicly available SARS-CoV-2 data to combat the pandemic

Researchers at the Department of Computer Science publish a new study

The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure, molecular interactions, mutations and variants, and facilitated vaccine development and drug reuse studies and design. The European COVID-19 Data Platform was launched to support this data sharing, and has resulted in the deposition of several million SARS-CoV-2 raw reads. Dr. Björn Grüning und Dr. Wolfgang Maier from the Galaxy Team Freiburg (https://galaxyproject.org/eu, Bioinformatics, Prof. Rolf Backofen) were involved in a team who published now their work about (1) open data sharing, (2) tools for submission, analysis, visualization and data claiming (e.g. ORCiD), (3) the systematic analysis of these datasets, at scale via the SARS-CoV-2 Data Hubs as well as (4) lessons learnt. The European Galaxy Server https://usegalaxy.eu was used to develop Galaxy workflows for the SARS-CoV-2 data analysis. This paper describes a component of the Platform, the SARS-CoV-2 Data Hubs, which enables the extension and set up of infrastructure that is intended to use more widely in the future for pathogen surveillance and pandemic preparedness.

All activities around the Covid data analysis, tools, workflows, and training material can be found on the special Covid website of the Galaxy project https://galaxyproject.org/projects/covid19.

Rahman,N. et al. (2024) Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses. Microbial Genomics, 10. https://doi.org/10.1099/mgen.0.001188

Contact:

Dr. Björn Grüning
Head of Freiburg Galaxy Team
Bioinformatics
Department of Computer Science
University of Freiburg
E-Mail: gruening@informatik.uni-freiburg.de

Dr. Anika Erxleben-Eggenhofer
Project Management, Teaching and Training Coordination
Bioinformatics
Department of Computer Science
University of Freiburg
E-Mail: erxleben@informatik.uni-freiburg.de

Kerstin Steiger-Merx
Representative PR/Marketing
Faculty of Engineering
University of Freiburg
Tel.: 0761/203-8056
E-Mail: steiger-merx@tf.uni-freiburg.de