Table 1 Comparison of runtimes (wall times) for all datasets used in the assembly benchmark. All tools were run with 16 threads, except for Haploflow, which did not support multi-threading. Values are given in [hh]:mm:ss. “-”: assemblers did not produce any results. Values marked with a are lower bounds because the tools did not finish on all samples
From: Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs
Dataset/tool | HRV in silico mixture | HIV1 in silico mixture | Metatranscriptomic dataset | ||
|---|---|---|---|---|---|
1× | 10× | 100× | |||
PenguiN | 00:08 | 00:18 | 00:03:34 | 00:25:40 | 89:17:51 |
Megahit | 00:03 | 00:33 | 00:03:14 | 00:08:36 | 28:39:21 |
metaSPAdes | 00:19 | 02:14 | 01:02:34 | 02:12:02 | 668:47:30 |
metaviralSPAdes | 00:23 | 01:02 | 00:04:03 | 00:13:39 | - |
rnaSPAdes | 00:08 | 00:27 | 00:02:14 | 00:08:06 | 34:28:50 |
rnaviralSPAdes | 00:11 | 00:37 | 00:03:32 | 00:10:08 | 31:31:44 |
SAVAGE | 01:41 | 25:27 | - | - | - |
IVA | 03:04 | 04:31 | 00:51:31 | 29:17:30 | - |
VICUNA | 00:02 | 00:33 | 03:28:33 | 29:31:19 | a4989:38:20 |
Haploflow | 00:02 | 00:47 | 00:03:41 | - | a568:57:30 |