VEO report on mutations and variation in publicly shared SARS-CoV-2 raw sequencing data.

14 April 2022

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In its eleventh report to the European Commission, VEO Consortium members summarize mobilisation and analysis of SARS-CoV-2 sequence data submitted to the European COVID-19 Data Platform in the context of the VEO project, which aims to develop tools and data analytics for pandemic and outbreak preparedness.

Summary:

  • Since the last update, there has been a modification in the workflow of data analyses that are foundational for this report. This was necessary because of the rapidly increasing size of data.
  • A major step forward is that the COVID-19 Data Portal now provides SARS-CoV-2 sequence data and analysis tools via a new feature, the CoVEO app (https://www.covid19dataportal.org/coveo). That means that the analyses include variant calling (filtered and unfiltered) and assembly that were developed and fine tuned by VEO partners, now run on EMBL-EBI’s high performance compute infrastructure. The results of these workflows are archived, indexed and available through the COVID-19 Data Portal for browsing and download: https://www.covid19dataportal.org/sequences?db=sra-analysis-covid19
  • The CoVEO app interprets and summarizes the variation data produced by these pipelines. Here, users can explore the emergence, spread and incidence of SARS-CoV-2 variants across the globe to give a view of the status of the pandemic. This app can be accessed by clicking the ‘Variant Browser’ links throughout the COVID-19 Data Portal.

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