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Edits by Patrick for following sections: DivBrowse, Acknowledgements,…
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#### DivBrowse | ||
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<!-- Sebastian B --> | ||
<!-- Sebastian B and Patrick K --> | ||
[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 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 and can handle hundreds of millions of variants across thousands of samples. | ||
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. | ||
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DivBrowse employs the BrAPI-Genotyping module to access genotypic data from external BrAPI endpoints. | ||
DivBrowse also has an interface to [BLAST](https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi) [@doi:10.1016/S0022-2836(05)80360-2], 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 also has an interface to BLAST+ tools [@doi:10.1186/1471-2105-10-421] installed on Galaxy servers [@doi:10.1186/s13742-015-0080-7], which can be used to directly access genes or other genomic features from results of custom BLAST query. | ||
DivBrowse employs the BrAPI-Genotyping module to serve genotypic data as a BrAPI endpoint and to get genotypic data from other BrAPI endpoints. |
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