Tools for Assembly & Submission of SARS-CoV-2 Data
During the COVID-19 pandemic, ELIXIR Belgium contributed to the efforts in developing tools for analysis and exposure of viral data. We developed tools and guidance to facilitate submission of viral sequences to the European Nucleotide Archive (ENA). We currently maintain a dedicated Galaxy instance and a container to assemble and submit SARS-CoV-2 genomes to the ENA.
We used these tools to broker the submission of SARS-CoV-2 raw reads data from Belgian patients to ENA on behalf of the Institute of Tropical Medicine and the Universite Libre de Bruxelles. Additionally, ELIXIR Estonia integrated the Galaxy submission tool into their submission pipeline and has used it to submit thousands of raw read datasets to the ENA in the context of the PARI project.
We are actively involved in setting up best practices for the analysis of SARS-CoV-2 data through Galaxy using publicly accessible infrastructure and workflows.
ELIXIR Belgium is a partner in BY-COVID, a European project set up to mobilise all types of COVID-19 data and to build the infrastructure and know-how needed to deal with the next infectious disease epidemic. ELIXIR Belgium co-leads the work package focusing on data analysis tools. Additionally, we participate in and contribute to the EMBL/EC COVID-19 data platform meetings and as such help to shape the Belgian COVID-19 data efforts.