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@ARTICLE{Knig:1006993,
      author       = {König, Patrick and Beier, Sebastian and Mascher, Martin
                      and Stein, Nils and Lange, Matthias and Scholz, Uwe},
      title        = {{D}iv{B}rowse—interactive visualization and exploratory
                      data analysis of variant call matrices},
      journal      = {GigaScience},
      volume       = {12},
      issn         = {2047-217X},
      address      = {Oxford},
      publisher    = {Oxford University Press},
      reportid     = {FZJ-2023-01932},
      pages        = {giad025},
      year         = {2023},
      abstract     = {Background: The sequencing of whole genomes is becoming
                      increasingly affordable. In this context, large-scale
                      sequencing projectsare generating ever larger datasets of
                      species-specific genomic diversity. As a consequence, more
                      and more genomic data need to bemade easily accessible and
                      analyzable to the scientific community.Findings: We present
                      DivBrowse, a web application for interactive visualization
                      and exploratory analysis of genomic diversity datastored in
                      Variant Call Format (VCF) files of any size. By seamlessly
                      combining BLAST as an entry point together with interactive
                      dataanalysis features such as principal component analysis
                      in one graphical user interface, DivBrowse provides a novel
                      and unique setof exploratory data analysis capabilities for
                      genomic biodiversity datasets. The capability to integrate
                      DivBrowse into existing webapplications supports
                      interoperability between different web applications.
                      Built-in interactive computation of principal
                      componentanalysis allows users to perform ad hoc analysis of
                      the population structure based on specific genetic elements
                      such as genes andexons. Data interoperability is supported
                      by the ability to export genomic diversity data in VCF and
                      General Feature Format 3 files.Conclusion: DivBrowse offers
                      a novel approach for interactive visualization and analysis
                      of genomic diversity data and optionally alsogene annotation
                      data by including features like interactive calculation of
                      variant frequencies and principal component analysis. Theuse
                      of established standard file formats for data input supports
                      interoperability and seamless deployment of application
                      instancesbased on the data output of established
                      bioinformatics pipelines.},
      cin          = {IBG-4},
      ddc          = {610},
      cid          = {I:(DE-Juel1)IBG-4-20200403},
      pnm          = {2171 - Biological and environmental resources for
                      sustainable use (POF4-217) / de.NBI (deNBI) / DFG project
                      491250510 - Open-Access-Publikationskosten / 2022-2024 /
                      Leibniz-Institut für Pflanzengenetik und
                      Kulturpflanzenforschung (IPK), Gatersleben (491250510)},
      pid          = {G:(DE-HGF)POF4-2171 / G:(DE-Juel-1)deNBI /
                      G:(GEPRIS)491250510},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {37083938},
      UT           = {WOS:001023598000001},
      doi          = {10.1093/gigascience/giad025},
      url          = {https://juser.fz-juelich.de/record/1006993},
}