Table 2. Execution Time.
| Read set/Tool | Total Time (fastq to bam) | Hours | Memory (GB) |
| Sample 1 | |||
| JAGuaR | 4206 | 70.10 | 0.8 (9)** |
| JAGuaR* | 905 | 15.08 | 0.8 (9)** |
| GSNAP | 4872 | 81.20 | 17.9 |
| MapSplice2 | 4493 | 74.88 | 5.3 |
| TopHat2 | 2540 | 42.33 | 3.5 |
| Sample 2 | |||
| JAGuaR | 3634 | 60.57 | 0.8 (9)** |
| JAGuaR* | 296 | 4.93 | 0.8 (9)** |
| GSNAP | 3974 | 66.23 | 17.9 |
| MapSplice2 | 1698 | 28.30 | 5.3 |
| TopHat2 | 1636 | 27.27 | 3.5 |
| Sample 3 | |||
| JAGuaR | 2363 | 39.38 | 0.8 (9)** |
| JAGuaR* | 513 | 8.55 | 0.8 (9)** |
| GSNAP | 2977 | 49.62 | 17.9 |
| MapSplice2 | 3037 | 50.62 | 5.3 |
| TopHat2 | 1593 | 26.55 | 3.5 |
*BWA-MEM algorithm.
**BWA memory.
Comparison of execution time and memory usage. All tools were run on a node with 64 GB memory with no other applications running.