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CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance.
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.
  • Wittig A; Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
  • Miranda F; Methods Development, Research Infrastructure and Information Technology (MFI), Bioinformatics and Systems Biology, Robert Koch Institute, Berlin, Germany.
  • Hölzer M; Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
  • Altenburg T; Methods Development, Research Infrastructure and Information Technology (MFI), Bioinformatics and Systems Biology, Robert Koch Institute, Berlin, Germany.
  • Bartoszewicz JM; Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
  • Beyvers S; Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
  • Dieckmann MA; Methods Development, Research Infrastructure and Information Technology (MFI), Bioinformatics and Systems Biology, Robert Koch Institute, Berlin, Germany.
  • Genske U; Department of Biology and Chemistry, Justus-Liebig-University Gießen, Gießen 35390, Germany.
  • Giese SH; Department of Biology and Chemistry, Justus-Liebig-University Gießen, Gießen 35390, Germany.
  • Nowicka M; Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
  • Richard H; Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
  • Schiebenhoefer H; Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
  • Schmachtenberg AJ; Methods Development, Research Infrastructure and Information Technology (MFI), Bioinformatics and Systems Biology, Robert Koch Institute, Berlin, Germany.
  • Sieben P; Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
  • Tang M; Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
  • Tembrockhaus J; Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
  • Renard BY; Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
  • Fuchs S; Department of Human Genetics, Hannover Medical School, Hannover 30625, Germany.
Bioinformatics ; 38(17): 4223-4225, 2022 Sep 02.
Article in English | MEDLINE | ID: covidwho-1922197
ABSTRACT

SUMMARY:

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. AVAILABILITY AND IMPLEMENTATION CovRadar is freely accessible at https//covradar.net, its open-source code is available at https//gitlab.com/dacs-hpi/covradar. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Topics: Variants Limits: Humans Language: English Journal: Bioinformatics Journal subject: Medical Informatics Year: 2022 Document Type: Article Affiliation country: Bioinformatics

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Topics: Variants Limits: Humans Language: English Journal: Bioinformatics Journal subject: Medical Informatics Year: 2022 Document Type: Article Affiliation country: Bioinformatics