Table 5.
Running time and memory requirements on the HG002 High confidence SV set.a
| Tool | Running time (min) |
Memory (Go) | ||
|---|---|---|---|---|
| Total | Mapping | Genotyping | ||
| SVJedi-graph | 29.7 | 24.8 | 4.3 | 19.1 |
| cuteSV | 201.9 | 176 | 25.9 | 65.2 (cuteSV) |
| LRcaller | 196.6 | 176 | 20.6 | 29.2 (minimap2) |
| Sniffles2 | 233.9 | 176 | 57.9 | 29.2 (minimap2) |
| SVJedi | 189.9 | 181.9 | 7.5 | 13.9 |
a
All tools were run on 20 CPU threads when multi-threading was supported (all but Sniffles2). The total running time shown for SVJedi-graph and SVJedi includes the SV representation step (allelic linear sequences for SVJedi and variation graph for SVJedi-graph) in addition to the mapping and genotyping time. The memory requirement shown for cuteSV, Sniffles2 and LRcaller is the maximum amount of memory used by either the genotyper or minimap2.