Table 5.
Running speed, accuracy, and specificity of AS detection tools.
| Tool | Data Source | Running Time (Minutes) |
Maximum
Memory (GB) |
Maximum CPU (%) | Number of SJs |
Number of
Differentially Spliced Isoforms |
|---|---|---|---|---|---|---|
| Alt Event Finder | ENCODE | 12 | 1.364 | 100 | 30569 | N/A |
| SpliceMap | ENCODE | 42 | 3.1 | 99.9 | 11882 | N/A |
| FineSplice | ENCODE | 2 | 1.364 | 100 | 8577 | N/A |
| RSW | N/A | N/A | N/A | N/A | N/A | N/A |
| RSR | ENCODE | 24 | 3.968 | 100 | 3143 | N/A |
| PASTA | ENCODE | 350 | 2.17 | 101 | 14675 | N/A |
| rMATS | mouse used in RSW study | 44 | 26.536 | 274 | N/A | 17 |
| SOAPsplice | ENCODE | 123 | 5.332 | 99.7 | 10381 | N/A |
| SplicePie | N/A | N/A | N/A | N/A | N/A | N/A |
| SplicingCompass | N/A | N/A | N/A | N/A | N/A | N/A |
| TopHat | ENCODE | 1.75 | 1.364 | 100 | 9619 | N/A |
| TrueSight | ENCODE | 229 | 2.914 | 571 | 12360 | N/A |
| NSMAP | N/A | N/A | N/A | N/A | N/A | N/A |
| rSeqDiff | mouse used in RSW study | 115 | 0.186 | 119 | N/A | 203 |
| rSeqNP | N/A | N/A | N/A | N/A | N/A | N/A |