Table 1 Time, memory, final disk space, nodes, edges, total connected components and connected components with more than 1% of base pairs comparison of Bifrost, mdbg, pggb, Minigraph and Minigraph-Cactus for different number of haplotypes in input. Minigraph-Cactus times include the Minigraph graph construction step. pggb was not able to complete its execution on the largest dataset in more than 2 weeks thus it is not considered. Minigraph-Cactus failed to compute the 104 HAP dataset
From: Comparing methods for constructing and representing human pangenome graphs
Haplotypes | Metric | Bifrost | pggb | Minigraph | Minigraph-Cactus | mdbg |
|---|---|---|---|---|---|---|
2 | Time (hh:mm:ss) | 1:21:25 | 15:45:30 | 00:08:33 | 3:11:59 | 00:02:38 |
Memory (GB) | 53 | 24 | 38 | 66 | 8 | |
Disk space (GB) | 4.8 | 4.3 | 2.9 | 3.6 | 4.4 | |
Nodes | 9482 k | 8492 k | 34 k | 10,851 k | 17 k | |
Edges | 13,108 k | 11,503 k | 48 k | 14,702 k | 23 k | |
Conn comp | 2 | 1402 | 25 | 4 | 174 | |
Conn comp > 1% bp | 1 | 30 | 24 | 4 | 24 | |
10 | Time (hh:mm:ss) | 2:27:29 | 117:08:09 | 2:03:29 | 15:57:05 | 00:05:46 |
Memory (GB) | 102 | 71 | 49 | 154 | 18 | |
Disk space (GB) | 12 | 7.6 | 2.9 | 7 | 9.7 | |
Nodes | 27,468 k | 29,315 k | 133 k | 37,767 k | 67 k | |
Edges | 37,584 k | 40,282 k | 190 k | 51,595 k | 93 k | |
Conn comp | 3 | 864 | 25 | 3 | 40 | |
Conn comp > 1% bp | 1 | 5 | 24 | 3 | 1 | |
104 | Time (hh:mm:ss) | 18:38:28 | — | 46:22:00 | — | 00:31:38 |
Memory (GB) | 122 | — | 61 | — | 39 | |
Disk space (GB) | 29.4 | — | 3.2 | — | 38 | |
Nodes | 106,339 k | — | 632 k | — | 270 k | |
Edges | 293,839 k | — | 912 k | — | 396 k | |
Conn comp | 17 | — | 25 | — | 1097 | |
Conn comp > 1% bp | 1 | — | 24 | — | 1 |