JBrowse 2 visualizations gallery

Below are some examples of the visualizations JBrowse 2 has to offer. For live demos, have a look at the demos page.

A genome vs genome dotplot displayed in the DotplotView. This displays grape vs peach genomes via PAF file

A linear synteny display for grape vs peach displayed in the LinearSyntenyView via MCScan anchors file results

Shows sorting the alignments pileup by the base-pair-at-the-given-position in the AlignmentsTrack

Shows rendering of a .hic file type in the HicTrack

Screenshot of the SV inspector displaying inter-chromosomal translocations in the SKBR3 cell line. The SV inspector is a tabular view plus whole-genome circular overview of the SVs

Shows the ability to horizontally flip the current view. This allows the anti-sense strand to be read left to right

Using the synteny view to render a long-read vs the reference genome. This is available simply by clicking an alignments feature and selecting "Linear read vs ref"

Using the dotplot view to render a long-read vs the reference genome. This is available by right-clicking an alignments feature and selecting "Dotplot read vs ref"

This is a whole-genome overview of CNV data using a BigWig file of read-coverage depth. This uses the XYPlot, with fill turned off. The BigWig data is binned at this resolution, and the blue shades represent the min, mean, and max value in each bin

Image of the "breakpoint split view" which examines the breakpoints of a structural variant, e.g. an interchromosomal translocation, and connects supporting reads (black splines) and the variant call itself (green thicker line, with feet indicating directionality)

Screenshot showing a heterozygous small deletion in the GIAB dataset. The nanopore reads are colored and sorted by the HP (haplotype) tag which helps show that the deletion is exclusive to one haplotype. Users can color, sort, group, and filter by tags (live link)

Screenshot showing a ~1.5kb insertion in the GIAB dataset, with Nanopore, PacBio, and Illumina reads. This screenshot shows the "Show soft clipping" option enabled on the Illumina reads, which helps reveal the boundaries of the insertion on the short reads, while the long reads fully span the insertion (live link)

Screenshot showing a ~500bp insertion from SKBR3 (breast cancer) cell line PacBio reads. Users can right-click sequence reads, then click "read vs reference" to show complex read alignments in a "synteny style" view (lower panel). Users can also interactively get the sequence of read portions with a click-and-drag action (lower panel, in blue) (live link)

A methylated and unmethylated CpG island shown using the MM tag with nanopore reads on the COLO829 (melanoma) cancer cell line. This dataset (live link)

An example of the 1000 genomes structural variant call VCF, showing a large inversion on chromosome 19. This screenshot used the in-app clustering workflow on the inverted region, and then zoomed out further (live link)