Table 2.
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) |
-
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.
