Table 3.
Running time and memory usage of quantification methods on SE and PE data
| SE | PE | |||||||
|---|---|---|---|---|---|---|---|---|
| Method | Alignment time | Quant. time | Total time | Peak Memory | Alignment time | Quant. time | Total time | Peak Memory |
| RSEM | 24 | 50 | 74 | 1.1 | 15 | 50 | 66 | 1.1 |
| IsoEM | 5 | 6 | 12 | 12 | 14 | 10 | 24 | 14 |
| Cufflinks | 33 | 3 | 36 | 2.0 | 60 | 6 | 66 | 2.0 |
| rQuant | 33 | 183 | 216 | 2.0 | ||||
| RSEM v0.6 | 9 | 22 | 31 | 1.1 | ||||
The alignment time, quantification time, total time, and peak memory usage of the tested quantification methods on SE and PE simulated data sets with 20 million fragments. Times are in minutes and memory is specified in GB.