Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

Franziska Hufsky(Friedrich Schiller University Jena), Kevin Lamkiewicz(Friedrich Schiller University Jena), Alexandre Almeida(European Bioinformatics Institute), Abdel Aouacheria(Centre National de la Recherche Scientifique), Cecilia N. Arighi, Alex Bateman(European Bioinformatics Institute), Jan Baumbach(Technical University of Munich), Niko Beerenwinkel(ETH Zurich), Christian Brandt(Jena University Hospital), Marco Cacciabue(Consejo Nacional de Investigaciones Científicas y Técnicas), Sara Chuguransky(European Bioinformatics Institute), Oliver Drechsel(Robert Koch Institute), ROBERT FINN, Adrian Fritz(Helmholtz Centre for Infection Research), Stephan Fuchs(Robert Koch Institute), Georges Hattab(Philipps University of Marburg), Anne-Christin Hauschild(Philipps University of Marburg), Dominik Heider(Philipps University of Marburg), Marie Hoffmann(Freie Universität Berlin), Martin Hölzer(Friedrich Schiller University Jena), Stefan Hoops(Biocom), Lars Kaderali, Ioanna Kalvari, Max von Kleist(Robert Koch Institute), Renó Kmiecinski(Robert Koch Institute), Denise Kühnert(Max Planck Institute for the Science of Human History), Gorka Lasso(Albert Einstein College of Medicine), Pieter Libin(Hasselt University), Markus List(Technical University of Munich), Hannah F. Löchel(Philipps University of Marburg), María Martin(European Bioinformatics Institute), Roman Martin(Philipps University of Marburg), Julian Matschinske(Technical University of Munich), Alice C. McHardy(Helmholtz Centre for Infection Research), Pedro Mendes(University of Connecticut), Jaina Mistry(European Bioinformatics Institute), Vincent Navratil, Eric P. Nawrocki(National Center for Biotechnology Information), Áine O’Toole, Nancy Ontiveros‐Palacios(European Bioinformatics Institute), Anton I. Petrov(European Bioinformatics Institute), Guillermo Rangel-Piñeros(University of Copenhagen), Nicole Redaschi, Susanne Reimering(Biology of Infection), Knut Reinert(Freie Universität Berlin), Alejandro Reyes(Universidad de Los Andes), Lorna Richardson(European Bioinformatics Institute), David L Robertson(MRC University of Glasgow Centre for Virus Research), Sepideh Sadegh(Technical University of Munich), Joshua B. Singer(MRC University of Glasgow Centre for Virus Research), Kristof Theys(Rega Institute for Medical Research), Chris Upton(University of Victoria), Marius Welzel(Philipps University of Marburg), Lowri Williams(European Bioinformatics Institute), Manja Marz(Friedrich Schiller University Jena)
Briefings in Bioinformatics
October 30, 2020
10.1093/bib/bbaa232
Cited by 148Open Access
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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.

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