Table 1.

Basic information and functionality comparison between VRPG and other pangenome graph visualization tools

	VRPG	Bandage	GfaViz	gfaestus	Sequence TubeMap	MoMI-G	ODGI^a	PGR-TK^a	PanGraphViewer
Distributing license	MIT	GNU GPL v3	ISC	MIT	MIT	MIT	MIT	MIT	MIT
Supported operating system	Linux	Linux; MacOS; Windows	Linux; MacOS; Windows	Linux; MacOS	Linux; MacOS	Linux; MacOS	Linux	Linux; MacOS	Linux; MacOS; Windows
Supported pangenome graph format	GFAv1; rGFA	GFAv1; rGFA;	GFAv1; GFAv2; rGFA	GFAv1 (also needs ODGI's layout TSV)	xg; vg; gbz	xg	GFAv1; og	GFAv1	GFAv1; rGFA
Deployment	Web-based	Desktop-based	Desktop-based	Desktop-based	Web-based	Web-based	Desktop-based	Desktop-based	Web-based; Desktop-based
Rendering object	Subgraph	Full graph	Full graph	Full graph	Subgraph	Subgraph	Subgraph	Subgraph	Subgraph
Graph query mode	By coordinates	By node IDs	By node IDs	By node IDs	By coordinates; by node IDs	By coordinates	By coordinates	N/A	By coordinates
Rendering style	Dynamic	Dynamic	Dynamic	Dynamic	Dynamic	Dynamic	Static	Static	Dynamic
Support for annotation^b	BED; GFF3	TSV	N/A	BED; TSV	BED	BED; GFF3; WIG	N/A	N/A	BED; GFF3; GTF
Sequence-to-graph mapping	Yes (for graphs built by Minigraph)	Yes	N/A	N/A	N/A	N/A	N/A	N/A	N/A
Assembly-to-graph path highlighting	Yes	N/A	N/A	N/A	N/A	N/A	Yes (partial)	N/A	N/A
Assembly-specific node depth report	Yes	N/A	N/A	N/A	N/A	N/A	Yes (bin-based)	N/A	N/A

^aTools like ODGI and PGR-TK are multipurpose software suites, both of which perform graph visualization via their submodules. The function comparison list here only concerns their visualization module.
^bAlthough multiple tools accept user-supplied annotation files, they vary considerably regarding how they utilize these files with the graph.

Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration