Table 1.

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

VRPGBandageGfaVizgfaestusSequence TubeMapMoMI-GODGIaPGR-TKaPanGraphViewer
Distributing licenseMITGNU GPL v3ISCMITMITMITMITMITMIT
Supported operating systemLinuxLinux; MacOS; WindowsLinux; MacOS; WindowsLinux; MacOSLinux; MacOSLinux; MacOSLinuxLinux; MacOSLinux; MacOS; Windows
Supported pangenome graph formatGFAv1; rGFAGFAv1; rGFA;GFAv1;

GFAv2;

rGFA		GFAv1 (also needs ODGI's layout TSV)xg; vg; gbzxgGFAv1; ogGFAv1GFAv1; rGFA
DeploymentWeb-basedDesktop-basedDesktop-basedDesktop-basedWeb-basedWeb-basedDesktop-basedDesktop-basedWeb-based; Desktop-based
Rendering objectSubgraphFull graphFull graphFull graphSubgraphSubgraphSubgraphSubgraphSubgraph
Graph query modeBy coordinatesBy node IDsBy node IDsBy node IDsBy coordinates; by node IDsBy coordinatesBy coordinatesN/ABy coordinates
Rendering styleDynamicDynamicDynamicDynamicDynamicDynamicStaticStaticDynamic
Support for annotationbBED; GFF3TSVN/ABED; TSVBEDBED; GFF3; WIGN/AN/ABED; GFF3; GTF
Sequence-to-graph mappingYes (for graphs built by Minigraph)YesN/AN/AN/AN/AN/AN/AN/A
Assembly-to-graph path highlightingYesN/AN/AN/AN/AN/AYes (partial)N/AN/A
Assembly-specific node depth reportYesN/AN/AN/AN/AN/AYes (bin-based)N/AN/A

[i] 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.

[ii] bAlthough multiple tools accept user-supplied annotation files, they vary considerably regarding how they utilize these files with the graph.