DivBrowse is a software for interactive visualization and analysis of the diversity of genomic variants. It uses VCF and GFF3 files as data input and consists of a web server written in Python and a GUI written in Javascript. It is available as a Python package on PyPI.org.
Demo instances
Key facts
- Uses established bioinformatics file formats like VCF and GFF3 for data input
- Can handle very large VCF files up to 1 TB (gzip compressed)
- Configureable via YAML config file
- Filtering of variants by e.g. MAF, heterozygosity, QUAL-values
- Sorting of genotypes by name (alphabetical) and phylogenetic distance
- Counting of variants for each gene and their exons
- Built-in interactive analysis features like PCA, UMAP
- Export of VCF files
- Export of GFF3 files
Features
Filtering of variants
Quickly filter variants on calculated statistical measures like minor allele frequency, heterozygosity frequency or even QUAL values that come directly with the VCF file. Filter settings can also applied to data analysis features like the built-in principal component analysis and to the VCF export.
Zooming
The compressed view shows each genotype of the VCF as a one pixel high line. If your diversity panel contains of many genotypes, more genotypes can be visualized at once.
Minor allele frequency and heterozygosity calculation
The minor allele frequency and percentage of heterozygous calls of each variant is calculated ad-hoc for the given set of genotypes. The MAF is visualized in a horizontal heat map. The concrete MAF value can be obtained by moving the mouse cursor over the variant.
Gene catalogue and search
With the integrated gene catalogue you can browse and search all genes that are provided by your GFF3 file. The search can be restricted to a specific genomic region. You can directly jump to a gene without typing in or copy-and-paste genomic coordinates.
Sorting of genotypes
The list of genotypes can be sorted alphabetically or by the phylogenetic distance to the reference genome.
Interactive data analysis
The list of genotypes can be sorted alphabetically or by the phylogenetic distance to the reference genome.
Hierarchically-clustered heatmaps of distance matrices
Hierarchically-clustered heatmaps of distance matrices can be created based on custom genomic ranges of interest, e.g. for single genes, exons or even larger genomic regions.