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Wittig, Alice; Miranda, Fábio; Hölzer, Martin; Altenburg, Tom; Bartoszewicz, Jakub M; Beyvers, Sebastian; Dieckmann, Marius A; Genske, Ulrich; Giese, Sven H; Nowicka, Melania; Richard, Hugues; Schiebenhoefer, Henning; Schmachtenberg, Anna-Juliane; Sieben, Paul; Tang, Ming; Tembrockhaus, Julius; Renard, Bernhard Y; Fuchs, Stephan

CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance

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  • Media type: E-Article
  • Title: CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance
  • Contributor: Wittig, Alice; Miranda, Fábio; Hölzer, Martin; Altenburg, Tom; Bartoszewicz, Jakub M; Beyvers, Sebastian; Dieckmann, Marius A; Genske, Ulrich; Giese, Sven H; Nowicka, Melania; Richard, Hugues; Schiebenhoefer, Henning; Schmachtenberg, Anna-Juliane; Sieben, Paul; Tang, Ming; Tembrockhaus, Julius; Renard, Bernhard Y; Fuchs, Stephan
  • Published: Oxford University Press (OUP), 2022
  • Published in: Bioinformatics, 38 (2022) 17, Seite 4223-4225
  • Language: English
  • DOI: 10.1093/bioinformatics/btac411
  • ISSN: 1367-4803; 1367-4811
  • Origination:
  • Footnote:
  • Description: AbstractSummaryThe ongoing pandemic caused by SARS-CoV-2 emphasizes the importance of genomic surveillance to understand the evolution of the virus, to monitor the viral population, and plan epidemiological responses. Detailed analysis, easy visualization and intuitive filtering of the latest viral sequences are powerful for this purpose. We present CovRadar, a tool for genomic surveillance of the SARS-CoV-2 Spike protein. CovRadar consists of an analytical pipeline and a web application that enable the analysis and visualization of hundreds of thousand sequences. First, CovRadar extracts the regions of interest using local alignment, then builds a multiple sequence alignment, infers variants and consensus and finally presents the results in an interactive app, making accessing and reporting simple, flexible and fast.Availability and implementationCovRadar is freely accessible at https://covradar.net, its open-source code is available at https://gitlab.com/dacs-hpi/covradar.Supplementary informationSupplementary data are available at Bioinformatics online.
  • Access State: Open Access