Table 4.
Runtime and memory comparison between Merqury and KAT comp
| Assembly | Haploid (maternal) | Diploid (maternal, paternal, and combined) | ||||||
|---|---|---|---|---|---|---|---|---|
| Compute | CPU (h) | Max mem (GB) | CPU (h) | Max mem (GB) | ||||
| Function | Merqury | KAT | Merqury | KAT | Merqury | KAT | Merqury | KAT |
| Count k-mers in reads | 13.8 | 22.4 | 21.2 | 44.1 | 13.8 | 63.0 | 21.2 | 44.1 |
| Spectra-cn | 3.9 | 10.1 | 9.7 | 10.6 | ||||
| Spectra-asm, QV, Completeness | – | – | – | – | ||||
| Spectra-hap | 2.0 | – | 1.5 | – | 3.4 | – | 3.2 | – |
| Blobs, phase block, switch error | 2.8 | – | 10.3 | – | 5.6 | – | 8.1 | – |
| Total | 22.5 | 22.4 | 21.2 | 44.1 | 32.5 | 63.0 | 21.2 | 44.1 |
All statistics are from the haploid and diploid human genome NA12878 assembly. KAT comp was run once and three times to generate the equivalent spectra-cn plots generated with Merqury. In addition to the spectra-cn plots, Merqury simultaneously generates spectra-asm, QV and k-mer completeness statistics, which are not available in KAT. Runtimes were measured on Intel(R) Xeon(R) Gold 6140 CPU, with 2.30 GHz, using a maximum of 24 cores. CPU time is measuring runtime assuming a single core for comparison. Maximum memory footprint is reported in Max mem