Table 1.
Analysis of memory and runtime needed to produce the similarity matrixa
| ModDotPlot | StainedGlass | ||||||
|---|---|---|---|---|---|---|---|
| Sequence | n (mbp) | Plot Type | w (bp) | CPU time (s) | Memory (GB) | CPU time (s) | Memory (GB) |
| Human CHM13 Chr1 Centromere |
4.0 | Static | 4000 | 11.10 | 0.43 | 1871.31 | 12.95 |
| Interactive | 1000 | 204.85 | 1.16 | 2812.49 | 13.44 | ||
| Gibbon mSymSyn1 ChrY |
29.9 | Static | 32 000 | 51.16 | 2.05 | 9857.57 | 30.13 |
| Interactive | 8000 | 193.22 | 2.41 | 11 264.01 | 33.50 | ||
| Human HG002 ChrY |
62.5 | Static | 64 000 | 80.47 | 4.06 | 11 214.19 | 43.18 |
| Interactive | 16 000 | 269.84 | 5.90 | 14 806.91 | 48.95 | ||
|
Arabadopsis Col-CEN Whole Genome |
128.5 c = 5 |
Static | 32 000 | 289.12 | 6.13 | 16 014.17 | 33.41 |
| Interactive | 8000 | 1734.11 | 9.57 | 20 187.19 | 35.20 | ||
| Human CHM13 Whole Genome |
3117.3 c = 24 |
Static | 256 000 | 15 238.04 | 40.24 | — | — |
| Interactive | 64 000 | 29 101.76 | 44.31 | — | — |
a
This does not include plot runtime, as that is the same between StainedGlass and ModDotPlot. ModDotPlot was run with a target sketch size of m = 1000 for all samples. For the whole genome assemblies of Arabadopsis and CHM13, the runtime includes the comparative matrix between each pairwise combination of chromosomes, in addition to self-identity comparisons. StainedGlass was unable to complete CHM13 whole genome within 72 h of CPU time.