Fig. 1

JBrowse 2 integrates many views into a single application. A The Linear Genome View displaying gene annotations, quantitative signals, and a Hi-C track. B The Linear Genome View can provide a whole genome overview, here showing tumor vs normal sequencing coverage in the COLO829 cell line [17]. C The Circular View gives an overview of long-range relationships within and between chromosomes (here, they are translocations in an SKBR3 cancer genome). D The Dotplot View shows relationships between two sequences (in this case the relationship between hg19 and hg38 human genomes). E The Tabular View summarizes features in a sortable, filterable list, showing in this example the SKBR3 variant calls from Sniffles. F The Linear Synteny View shows relationships between two genomes (in this case, peach and grape) each of which is rendered using a Linear Genome View. G The SV Inspector allows inspection of structural variants by combining a Tabular View and a Circular View; here, both the Tabular and Circular views are visualizing a VCF file of translocations in an SKBR3 cancer genome called using Sniffles [18]. H The Breakpoint Split View shows events such as gene fusions and translocations (in this case, in the SKBR3 cancer genome) by aligning two Linear Genome Views and tracing the split or paired read mappings across the two views