Performance comparison between VRPG and other pangenome graph visualization tools
| Benchmarking task | Graph source | Graph type | Graph builder | Graph complexity (N:node; E:edge) | VRPGa | Bandage | GfaViz | PanGraphViewer |
|---|---|---|---|---|---|---|---|---|
| Graph parsing | Yeast | Full-graph | Minigraph | N: 37,062 E: 52,756 | 0.10 sec 64.80 MB | 3.50 sec 254.11 MB | 247.11 sec 2769.50 Mb | 0.22 sec 282.10 MB |
| Graph parsing | Human | Full-graph | Minigraph | N: 424,643 E: 637,628 | 0.07 sec 54.44 MB | 80.35 sec 10,066.50 MB | NA (memory cap) | 7.83 sec 524.38 MB |
| Minigraph-Cactus | N: 80,069,733 E: 110,938,345 | 0.10 sec 64.73 MB | NA (memory cap) | NA (memory cap) | NA (parsing error) | |||
| PGGB | N: 110,884,673 E: 154,756,169 | 0.09 sec 58.26 MB | NA (memory cap) | NA (memory cap) | NA (parsing error) | |||
| Graph parsing | Human | Subgraph > Chr 22 | Minigraph | N: 9545 E: 14,307 | 0.01 sec 62.5 MB | 1.80 sec 260.15 MB | 242.35 sec; 10,083.49 MB | 0.19 sec 307.11 MB |
| Minigraph-Cactus | N: 1,279,308 E: 1,780,703 | 0.01 sec 58.16 MB | 84.50 sec 2,120.66 MB | NA (memory cap) | 7.88 sec 815.58 MB | |||
| PGGB | N: 1,124,300 E: 1,568,024 | 0.02 sec 56.11 MB | 71.05 sec 1890.45 MB | NA (memory cap) | NA (parsing error) | |||
| Graph rendering | Yeast | Subgraph > Chr IV: 1–50,000 | Minigraph | N: 103 E: 142 | 0.02 sec 82.96 MB | 0.76 sec 105.94 MB | 0.12 sec 171.48 MB | 1.08 sec 323.73 MB |
| Subgraph > Chr IV: 1–500,000 | Minigraph | N: 1155 E: 1641 | 0.02 sec 194.86 MB | 1.51 sec 122.36 MB | 3.66 sec 324.79 MB | 1.68 sec 324.70 MB | ||
| Graph rendering | Human | Subgraph > Chr 22: 20,000,001–20,100,000 | Minigraph | N: 13 E: 18 | 0.01 sec 55.24 MB | 0.30 sec 103.70 MB | 0.16 sec 171.23 MB | 0.01 sec 255.26 MB |
| Minigraph-Cactus | N: 2248 E: 3106 | 0.05 sec 219.78 MB | 1.81 sec 129.66 MB | 13.25 sec 772.58 MB | 1.88 sec 339.91 MB | |||
| PGGB | N: 2252 E: 3116 | 0.05 sec 237.48 MB | 1.68 sec 129.81 MB | 14.15 sec 785.69 MB | NA (parsing error) | |||
| Subgraph > Chr 22: 20,000,001–20,500,000 | Minigraph | N: 288 E: 435 | 0.03 sec 82.78 MB | 1.33 sec 111.81 MB | 0.36 sec 181.08 MB | 1.29 sec 321.28 MB | ||
| Minigraph-Cactus | N: 21,982 E: 30,639 | 0.18 sec 605.82 MB | 19.12 sec 347.27 MB | NA (memory cap) | 7.37 sec 338.50 MB | |||
| PGGB | N: 66,132 E: 94,595 | 0.33 sec 1270.61 MB | 69.20 sec 766.10 MB | NA (memory cap) | NA (parsing error) |
[i] aThe format conversion (for Minigraph-Cactus and PGGB graphs) step and index building step were performed in advance and were not included in this benchmarking.