Table 3.
Index construction
| Tool | k | Build | Build | Mark | Mark | Total | Total | Mem | Mem |
|---|---|---|---|---|---|---|---|---|---|
| CPU | Wall | CPU | Wall | CPU | Wall | Final | Peak | ||
| Xengsort | 23 | 50 | 50 | 591 | 176 | 641 | 226 | 12.8 | 17.3 |
| Xengsort | 25 | 53 | 53 | 437 | 158 | 490 | 211 | 15.9 | 20.4 |
| Xengsort | 27 | 51 | 51 | 495 | 214 | 546 | 265 | 17.3 | 21.8 |
| Xenome | 25 | 992 | 151 | 2338 | 356 | 3626 | 552 | 31.2 | 57.1 |
| XenofilteR | – | – | – | – | – | 528 | 658 | 13.0 | 22.0 |
CPU times and wall clock times in minutes and memory in Gigabytes using different tools and different k-mer sizes for xengsort. “Build” times refer to collecting and hashing the k-mers according to species, but without marking weak k-mers. “Mark” times refer to marking weak k-mers. “Total” times are the sum of build and mark times, plus additional I/O times. “CPU” times measure total CPU work load (as reported by the time command as user time), and “wall” times refer to actually passed time. Final size (“mem final”) is measured by index size on disk (GB). Memory peak (“mem peak”) is the highest memory usage during construction (GB)