Journal Article

FZJ-2023-01932

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png DivBrowse—interactive visualization and exploratory data analysis of variant call matrices

König, P. (Corresponding author) ; Beier, S.FZJ* ; Mascher, M. ; Stein, N. ; Lange, M. ; Scholz, U.

2023
Oxford University Press Oxford

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Please use a persistent id in citations: http://hdl.handle.net/2128/34485  doi:10.1093/gigascience/giad025

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.

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Contributing Institute(s):

1. Bioinformatik (IBG-4)

Research Program(s):

1. 2171 - Biological and environmental resources for sustainable use (POF4-217) (POF4-217)
2. de.NBI (deNBI) (deNBI)
3. DFG project 491250510 - Open-Access-Publikationskosten / 2022-2024 / Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Gatersleben (491250510) (491250510)

Appears in the scientific report 2023

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