Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

Franziska Hufsky; Kevin Lamkiewicz; Alexandre Almeida; Abdel Aouacheria; Cecilia Arighi; Alex Bateman; Jan Baumbach; Niko Beerenwinkel; Christian Brandt; Marco Cacciabue; Sara Chuguransky; Oliver Drechsel; Robert D. Finn; Adrian Fritz; Stephan Fuchs; Georges Hattab; Anne-Christin Hauschild; Dominik Heider; Marie Hoffmann; Martin Hölzer; Stefan Hoops; Lars Kaderali; Ioanna Kalvari; Max von Kleist; René Kmiecinski; Denise Kühnert; Gorka Lasso; Pieter Libin; Markus List; Hannah F. Löchel; Maria J. Martin; Roman Martin; Julian Matschinske; Alice C. McHardy; Pedro Mendes; Jaina Mistry; Vincent Navratil; Eric Nawrocki; Áine Niamh O'Toole; Nancy Palacios-Ontiveros; Anton I. Petrov; Guillermo Rangel-Piñeros; Nicole Redaschi; Susanne Reimering; Knut Reinert; Alejandro Reyes; Lorna Richardson; David L. Robertson; Sepideh Sadegh; Joshua B. Singer; Kristof Theys; Chris Upton; Marius Welzel; Lowri Williams; Manja Marz

doi:10.20944/preprints202005.0376.v1

How to cite: Hufsky, F.; Lamkiewicz, K.; Almeida, A.; Aouacheria, A.; Arighi, C.; Bateman, A.; Baumbach, J.; Beerenwinkel, N.; Brandt, C.; Cacciabue, M.; Chuguransky, S.; Drechsel, O.; Finn, R.D.; Fritz, A.; Fuchs, S.; Hattab, G.; Hauschild, A.; Heider, D.; Hoffmann, M.; Hölzer, M.; Hoops, S.; Kaderali, L.; Kalvari, I.; von Kleist, M.; Kmiecinski, R.; Kühnert, D.; Lasso, G.; Libin, P.; List, M.; Löchel, H.F.; Martin, M.J.; Martin, R.; Matschinske, J.; McHardy, A.C.; Mendes, P.; Mistry, J.; Navratil, V.; Nawrocki, E.; O'Toole, Á.N.; Palacios-Ontiveros, N.; Petrov, A.I.; Rangel-Piñeros, G.; Redaschi, N.; Reimering, S.; Reinert, K.; Reyes, A.; Richardson, L.; Robertson, D.L.; Sadegh, S.; Singer, J.B.; Theys, K.; Upton, C.; Welzel, M.; Williams, L.; Marz, M. Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research. Preprints 2020, 2020050376 (doi: 10.20944/preprints202005.0376.v1). Hufsky, F.; Lamkiewicz, K.; Almeida, A.; Aouacheria, A.; Arighi, C.; Bateman, A.; Baumbach, J.; Beerenwinkel, N.; Brandt, C.; Cacciabue, M.; Chuguransky, S.; Drechsel, O.; Finn, R.D.; Fritz, A.; Fuchs, S.; Hattab, G.; Hauschild, A.; Heider, D.; Hoffmann, M.; Hölzer, M.; Hoops, S.; Kaderali, L.; Kalvari, I.; von Kleist, M.; Kmiecinski, R.; Kühnert, D.; Lasso, G.; Libin, P.; List, M.; Löchel, H.F.; Martin, M.J.; Martin, R.; Matschinske, J.; McHardy, A.C.; Mendes, P.; Mistry, J.; Navratil, V.; Nawrocki, E.; O'Toole, Á.N.; Palacios-Ontiveros, N.; Petrov, A.I.; Rangel-Piñeros, G.; Redaschi, N.; Reimering, S.; Reinert, K.; Reyes, A.; Richardson, L.; Robertson, D.L.; Sadegh, S.; Singer, J.B.; Theys, K.; Upton, C.; Welzel, M.; Williams, L.; Marz, M. Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research. Preprints 2020, 2020050376 (doi: 10.20944/preprints202005.0376.v1).

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 freely available online, either through web applications or public code repositories.

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Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

Abstract

Supplementary and Associated Material

Keywords

Subject

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