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#### DivBrowse

<!-- Sebastian B -->
[DivBrowse](https://divbrowse.ipk-gatersleben.de/) [@doi:10.1093/gigascience/giad025] is a web platform for exploratory data analysis of huge genotyping studies. The software can be run standalone or integrated as a plugin into existing data web portals. It provides a powerful interactive visualization of variant call matrices with hundreds of millions of variants and thousands of samples. It enables easy data import and export by using well established, standardized, bioinformatics file formats.
[DivBrowse](https://divbrowse.ipk-gatersleben.de/) [@doi:10.1093/gigascience/giad025] is a web platform for exploratory data analysis of large genotyping studies.
The software can be run standalone or integrated as a plugin into existing data web portals.
At its core, DivBrowse combines the convenience of a genome browser with features tailored to germplasm diversity analysis.
DivBrowse provides visual access to VCF files obtained through genotyping experiments.
It is able to display genomic features such as nucleotide sequence, associated gene models, and short genomic variants. DivBrowse also calculates and displays variant statistics such as minor allele frequencies, the proportion of heterozygous calls, and the proportion of missing variant calls.
Dynamic principal component analyses can be performed on a user-specified genomic area to provide information on local genomic diversity.

At its core, DivBrowse combines the convenience of a genome browser with features tailored to the diversity analysis of germplasm. It is able to display genomic features such as nucleotide sequence, associated gene models, and short genomic variants. DivBrowse provides visual access to large VCF files obtained through genotyping experiments. In addition, DivBrowse also calculates and displays variant statistics such as minor allele frequencies, proportion of heterozygous calls, and proportion missing variant calls. Dynamic Principal Component Analyses (PCA) can be performed on a user specified genomic area to provide information on local genomic diversity.

Parts of the BrAPI Genotyping module are implemented in DivBrowse. There is a server-side component which provides genotypic data that the DivBrowse database can consume. There is also a client-side GUI component which can visualize genotypic data via any external BrAPI endpoint. In addition to BrAPI, DivBrowse has an internal API to control the tool from a hosting web portal. DivBrowse also has an interface to BLAST, which can be used to directly access genes or other genomic features. The modular structure of DivBrowse allows developers to configure and easily embed links to other external information systems.
DivBrowse employs the BrAPI Genotyping module to access genotypic data from external BrAPI endpoints.
DivBrowse also has an interface to BLAST, which can be used to directly access genes or other genomic features.
The modular structure of DivBrowse allows developers to configure and easily embed links to other external information systems.

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