ELIXIR-CONVERGE D9.1 Report on mobilised sequence and variation data - relates to tasks 9.1-9.2

Mobilisation of SARS-CoV-2 data is a key output of the European COVID-19 Data Platform - which makes genomic and other biological data types, analysis and visualisation tools relating to SARS-CoV-2 freely available for the global scientific community. Sharing viral genome and variation data from around the world helps enable tracking of pathogen evolution, transmission and outbreak investigation, and ultimately contributes to the development of therapeutics. However, it is data mobilisation at scale which truly helps effective genomic surveillance take place. National sequencing centres are often prime candidates for this, as they can generate high volumes of genomic data over a long time period.

The scope of this deliverable was to maximise the mobilisation of SARS-CoV-2 sequence and variation data from national sequencing efforts as well as individual centres/labs into the European COVID-19 Data Platform. To achieve this, several aspects of user support were strengthened (including outreach to public health authorities) in addition to continuing the systematic analysis of raw SARS-CoV-2 reads in the INSDC as part of WP8. 

Through the work described in this deliverable, EMBL-EBI helped support SARS-CoV-2 sequence data streams with national submitters (to encourage open sharing of data beyond SARS-CoV-2). Through WP8 designed analysis workflows, we also generated >3 million variant calls which not only present across the European COVID-19 Data Platform but also other integrated EBI resources for increased visibility and access.