Table 1.
Upper half of the table shows construction time and memory requirements for BWA, kallisto and pufferfish (dense and sparse) on three different datasets
| Tool | Memory (MB) |
Time (h:m:s) |
||||
|---|---|---|---|---|---|---|
| Human transcriptome | Human genome | Bacterial genomes | Human transcriptome | Human genome | Bacterial genomes | |
| BWA | 292 | 4443 | 32 213 | 0:02:56 | 0:58:27 | 13:11:45 |
| Kallisto | 3552 | 150 657 | 315 387 | 0:03:05 | 3:27:42 | 9:07:35 |
| Pufferfish dense | 1466 | 27 438 | 75 342 | 0:04:13 | 2:09:25 | 13:10:00 |
| Pufferfish sparse | 1466 | 27 438 | 75 342 | 0:04:41 | 2:28:53 | 13:46:11 |
| TwoPaCo | 1466 | 9380 | 17 407 | 0:02:47 | 0:34:43 | 9:59:05 |
| Pufferize | 584 | 27 438 | 75 342 | 0:0:10 | 0:21:53 | 1:03:17 |
| Pufferfish dense index | 438 | 20 000 | 50 459 | 0:01:16 | 0:51:20 | 2:07:38 |
| Pufferfish sparse index | 331 | 17 745 | 50 457 | 0:01:44 | 1:10:48 | 2:43:49 |
In the lower half of the table, the construction statistics are provided for different phases of pufferfish pipeline. The time requirement for pufferfish is the sum of different subparts of the workflow, where the memory requirement is the max of the same. All of the tools in this table with the exception of TwoPaCo have single-threaded execution. We report here the timing results for running TwoPaCo with 16 threads. Timing results for TwoPaCo using a single thread are provided in Supplementary Table 4.