Table 3. Average runtimes per phase of the RNA-seq pipeline.
| Runtime and speedup per phase | |||||
|---|---|---|---|---|---|
| Pipeline | No. of nodes and cores | Pass 1 map | Rebuild genome | Pass 2 map | Variant calling steps |
| Classical pipeline | 1 node × single core | 1h 19min (n/a) | 4min (n/a) | 3h 29min (n/a) | 23h 1min (n/a) |
| 1 node × 20 cores | 6min (14.24×) | 2min (2.18×) | 22min (9.69×) | 12h 27min (1.85×) | |
| Halvade-RNA | 1 nodes × 20 cores | 14min (5.69×) | 4min (1.02×) | 39min (5.29×) | 2h 3min (11.21×) |
| 2 nodes × 20 cores | 8min (9.29×) | 4min (1.01×) | 22min (9.49×) | 1h 26min (16.04×) | |