Alice Wittig, Fabio Malcher Miranda, Martin Hölzer, Tom Altenburg, Jakub Maciej Bartoszewicz, Sebastian Beyvers, Marius Alfred Dieckmann, Ulrich Genske, Sven Hans-Joachim Giese, Melania Nowicka, Hugues Richard, Henning Schiebenhoefer, Anna-Juliane Schmachtenberg, Paul Sieben, Ming Tang, Julius Tembrockhaus, Bernhard Y. Renard, Stephan Fuchs
- The 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.
MetadatenAuthor details: | Alice WittigORCiD, Fabio Malcher MirandaORCiD, Martin HölzerORCiD, Tom AltenburgORCiD, Jakub Maciej BartoszewiczORCiDGND, Sebastian BeyversORCiD, Marius Alfred Dieckmann, Ulrich GenskeORCiD, Sven Hans-Joachim GieseORCiDGND, Melania NowickaORCiDGND, Hugues Richard, Henning SchiebenhoeferORCiD, Anna-Juliane SchmachtenbergGND, Paul Sieben, Ming Tang, Julius Tembrockhaus, Bernhard Y. RenardORCiDGND, Stephan Fuchs |
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DOI: | https://doi.org/10.1093/bioinformatics/btac411 |
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ISSN: | 1367-4803 |
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ISSN: | 1367-4811 |
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Pubmed ID: | https://pubmed.ncbi.nlm.nih.gov/35799354 |
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Title of parent work (English): | Bioinformatics |
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Subtitle (English): | continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance |
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Publisher: | Oxford Univ. Press |
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Place of publishing: | Oxford |
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Publication type: | Article |
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Language: | English |
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Date of first publication: | 2022/07/07 |
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Publication year: | 2022 |
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Release date: | 2024/04/10 |
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Volume: | 38 |
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Issue: | 17 |
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Number of pages: | 3 |
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First page: | 4223 |
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Last Page: | 4225 |
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Funding institution: | European Centers for Disease Control [ECDC] [2021/008 ECD.12222]; Bundesministerium für Bildung und Forschung [031L0175C, 01KI1905D]; Bundesministerium für Wirtschaft und Klimaschutz Daten-und KI-gestütztes; Frühwarnsystem zur Stabilisierung der deutschen Wirtschaft [01MK21009E]; German Network for Bioinformatics Infrastructure; de.NBI-cloud; [031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A,; 031A532B] |
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Organizational units: | Digital Engineering Fakultät / Hasso-Plattner-Institut für Digital Engineering GmbH |
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DDC classification: | 0 Informatik, Informationswissenschaft, allgemeine Werke / 00 Informatik, Wissen, Systeme / 004 Datenverarbeitung; Informatik |
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| 5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie |
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Peer review: | Referiert |
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Publishing method: | Open Access / Bronze Open-Access |
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