Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

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BeYond-COVID (BY-COVID) aims to provide comprehensive open data on SARS-CoV-2 and other infectious diseases across scientific, medical, public health and policy domains. It strongly emphasises mobilising raw viral sequences, helping to identify and monitor the spread of SARS-CoV-2 variants. The project further accelerates access to SARS-CoV-2 and COVID-19 and linking patient and research data.

To ensure interoperability of national and global efforts, BY-COVID enables federated data analysis compliant with data protection regulations, harmonise and manage metadata and sample identifiers, and facilitate long-term cataloguing.

In an unprecedented and unique interdisciplinary effort, BY-COVID brings together 53 partners from 19 countries and stakeholders from the biomedical field, hospitals, public health, social sciences and humanities.

Ultimately, it will improve European readiness for future pandemics, enhance genomic surveillance and rapid-response capabilities. In addition, BY-COVID serves as a demonstrator of interdisciplinary work across country borders. The project's outputs will allow scientists across multiple domains, including SMEs and industry, to access varied data with the potential to generate new knowledge on infectious diseases.

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Switzerland

Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

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These materials were developed in the context of the BY-COVID project, EU Grant Agreement 101046203, for the course module Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

Keywords: Mutation calling, viral genome, genome reconstruction, lineage assignment, clade assignment, SARS-CoV-2 sequencing data

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