Table 1 Runtime and memory consumption of Haploflow, SAVAGE in de novo mode (version 0.4.1), metaSPAdes (3.14), and MEGAHIT (1.2.9). Time and memory is averaged for the HCMV mixtures. SAVAGE did not successfully complete on the HCMV in vitro mixtures and the simulated virome data. Values were calculated using Linux’ time command
From: Haploflow: strain-resolved de novo assembly of viral genomes
Software/data set | HIV 3 in silico mixture | Â | HCMV in vitro mixture | Â | Simulated virome | Â |
|---|---|---|---|---|---|---|
Metric | CPU user time (seconds) | Memory peak (GB) | Avg. CPU user time (seconds) | Avg. memory peak (GB) | CPU user time (seconds) | Memory peak (GB) |
Haploflow | 724 | 0.009 | 5170 | 17.509 | 18,245 | 47.678 |
SAVAGE | 110,208 | 102.938 | 75,518 | 17.658 | – | – |
PEHaplo | 10,127 | 11.819 | 58,920 | 13.998 | – | – |
metaSPAdes | 1500 | 1.054 | 42,906 | 65.641 | 25,996 | 23.399 |
MEGAHIT | 250 | 0.269 | 2910 | 0.754 | 9,690 | 2.148 |