Franziska Hufsky1, Kevin Lamkiewicz1, Alexandre Almeida2, Abdel Aouacheria3, Cecilia Arighi4, Alex Bateman5, Jan Baumbach6, Niko Beerenwinkel7, Christian Brandt8, Marco Cacciabue9, Sara Chuguransky10, Oliver Drechsel11, Robert D Finn12, Adrian Fritz13, Stephan Fuchs11, Georges Hattab14, Anne-Christin Hauschild15, Dominik Heider16, Marie Hoffmann17, Martin Hölzer18, Stefan Hoops19, Lars Kaderali20, Ioanna Kalvari21, Max von Kleist11, Renó Kmiecinski11, Denise Kühnert22, Gorka Lasso23, Pieter Libin24, Markus List6, Hannah F Löchel15, Maria J Martin25, Roman Martin15, Julian Matschinske26, Alice C McHardy27, Pedro Mendes28, Jaina Mistry25, Vincent Navratil29, Eric P Nawrocki30, Áine Niamh O'Toole31, Nancy Ontiveros-Palacios25, Anton I Petrov25, Guillermo Rangel-Pineros32, Nicole Redaschi33, Susanne Reimering34, Knut Reinert17, Alejandro Reyes35, Lorna Richardson36, David L Robertson37, Sepideh Sadegh38, Joshua B Singer39, Kristof Theys40, Chris Upton41, Marius Welzel15, Lowri Williams42, Manja Marz18. 1. Friedrich-Schiller-University Jena, Germany. 2. EMBL-EBI and the Wellcome Sanger Institute, UK. 3. CNRS, France. 4. Biocuration and Literature Access at PIR, USA. 5. Protein Sequence Resources at EMBL-EBI, UK. 6. Technical University of Munich, Germany. 7. Computational Biology at ETH Zurich, Switzerland. 8. Institute of Infectious Disease and Infection Control at Jena University Hospital, Germany. 9. Consejo Nacional de Investigaciones Científicas y Tócnicas (CONICET) working on FMDV virology at the Instituto de Agrobiotecnología y Biología Molecular (IABiMo, INTA-CONICET) and at the Departamento de Ciencias Básicas, Universidad Nacional de Luján (UNLu), Argentina. 10. Pfam and InterPro databases, at the EMBL-EBI, UK. 11. bioinformatics department at the Robert Koch-Institute, Germany. 12. Pfam and MGnify. 13. Computational Biology of Infection Research group of Alice C. McHardy at the Helmholtz Centre for Infection Research, Germany. 14. Bioinformatics Division at Philipps-University Marburg, Germany. 15. Philipps-University Marburg, Germany. 16. Data Science in Biomedicine at the Philipps-University of Marburg, Germany. 17. Freie Universität Berlin, Germany. 18. Friedrich Schiller University Jena, Germany. 19. Biocomplexity Institute and Initiative at the University of Virginia, USA. 20. Bioinformatics and head of the Institute of Bioinformatics at University Medicine Greifswald, Germany. 21. Senior Software Developer. 22. Max Planck Institute for the Science of Human History. 23. Chandran Lab, Albert Einstein College of Medicine, USA. 24. University of Hasselt, Belgium. 25. EMBL-EBI, UK. 26. Chair of Experimental Bioinformatics at TU Munich, Germany. 27. Computational Biology of Infection Research Lab at the Helmholtz Centre for Infection Research in Braunschweig, Germany. 28. Center for Quantitative Medicine of the University of Connecticut School of Medicine, USA. 29. Bioinformatics and Systems Biology at the Rhône Alpes Bioinformatics core facility, Universitó de Lyon, France. 30. National Center for Biotechnology Information (NCBI). 31. Rambaut group at Edinburgh University, UK. 32. GLOBE Institute in the University of Copenhagen, Denmark. 33. Development of the Swiss-Prot group at the SIB for UniProt and SIB resources that cover viral biology (ViralZone). 34. Computational Biology of Infection Research group of Alice C. McHardy at the Helmholtz Centre for Infection Research. 35. Universidad de los Andes, Colombia. 36. Sequence Families team at EMBL-EBI, UK. 37. MRC-University of Glasgow Centre for Virus Research, UK. 38. Chair of Experimental Bioinformatics at Technical University of Munich, Germany. 39. MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK. 40. Rega institute of the University of Leuven, Belgium. 41. Department of Biochemistry and Microbiology, University of Victoria, Canada. 42. Pfam and InterPro databases, at EMBL-EBI, UK.
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:evbc@unj-jena.de.
SARS-CoV-2 (n class="Species">severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious diseaseCOVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:evbc@unj-jena.de.
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