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

Wittig, A., Miranda, F., Hölzer, M., Altenburg, T., Bartoszewicz, J. M., Beyvers, S., et al. (2022). CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance. Bioinformatics, 38(17), 4223-4225. doi:10.1093/bioinformatics/btac411.

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Item Permalink: https://hdl.handle.net/21.11116/0000-000E-5667-E Version Permalink: https://hdl.handle.net/21.11116/0000-000E-5668-D
Genre: Journal Article

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 Creators:
Wittig , Alice , Author
Miranda , Fábio, Author
Hölzer, Martin, Author
Altenburg, Tom1, Author                 
Bartoszewicz, Jakub M. , Author
Beyvers, Sebastian , Author
Dieckmann, Marius A. , Author
Genske, Ulrich , Author
Giese, Sven H. , Author
Nowicka, Melania1, Author                 
Richard, Hugues , Author
Schiebenhoefer, Henning , Author
Schmachtenberg, Anna-Juliane , Author
Sieben, Paul, Author
Tang, Ming, Author
Tembrockhaus, Julius , Author
Renard, Bernhard Y. , Author
Fuchs, Stephan , Author
Affiliations:
1IMPRS for Biology and Computation (Anne-Dominique Gindrat), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479666              

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 Abstract: 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.

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Language(s): eng - English
 Dates: 2022-06-132022-07-072022-09
 Publication Status: Issued
 Pages: -
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 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1093/bioinformatics/btac411
PMID: 35799354
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Title: Bioinformatics
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 38 (17) Sequence Number: - Start / End Page: 4223 - 4225 Identifier: ISSN: 1367-4803
CoNE: https://pure.mpg.de/cone/journals/resource/954926969991