Table 3.
Runtime and memory usage of error correction pipelines.
| Dataset | pychopper | isONclust | isONcorrect | RATTLE cluster | RATTLE correct | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| Peak memory | Runtime | Peak memory | Runtime | Peak memory | Runtime | Peak memory | Runtime | Peak memory | Runtime | |
| Drosophila | 5 Gb | 32 min | 34 Gb | 2 h 05 min | 102 Gb | 43 h 54 min | 48 Gb | 16 h 52 min | 314 Gb | 1 h 34 min |
| SIM-ca | – | – | 8 Gb | 0 h 08 min | 99 Gb | 1 h 40 min | 2 Gb | 14 min | 83 Gb | 9 min |
| SIRV | 3 Gb | 14 min | 10 Gb | 0 h 9 min | 127 Gb | 6 h 13 min | 19 Gb | 28 min | 18 Gb | 49 min |
| SIM-full | – | – | 49 Gb | 2 h 13 min | 385 Gb | 54 h 49 min | 108 Gb | 1 h 29 min | – | – |
| ONT-old | – | – | 24 Gb | 4 h 43 min | 89 Gb | 11 h 11 min | 14 Gb | 11 h 51 min | 14 Gb | 23 min |
RATTLE correct on SIM-full did not complete because it exceeded the 500 Gb memory capacity of our server (we tried using 1, 2, 4, 8, 16, 32, and 60 cores).