Table 2.
Results of Bowtie2 alignment of dataset 1 showing raw data and the trimmed data by each tool
| Dataset/alignment | Reads | Alignment (paired)a | Run timeb (s) |
|---|---|---|---|
| Tolerant alignment | |||
| Unfiltered | 11 008 190 | 9 018 810 (8,323,786) | N/A |
| Fastx-Toolkit | 9 631 977 | 8 073 757 (N/A) | 670.1/356.3 |
| Reaper | 9 428 331 | 9 057 448 (N/A) | 324.8/166.8 |
| Cutadapt | 9 456 172 | 9 127 667 (N/A) | 342.5/176.7 |
| EA-Utils | 8 995 134 | 8 662 596 (8 578 790) | 9.3/8.0 |
| Scythe/Sickle | 9 453 459 | 9 133 464 (8 636 984) | 529.3/279.7 |
| AdapterRemoval | 9 456 350 | 9 147 915 (8 689 668) | 960.2 |
| Trimmomatic SW | 9 456 819 | 9 150 361 (8 693 000) | 33.7/9.6 |
| Trimmomatic MI | 9 456 819 | 9 153 375 (8 697 690) | 34.3/9.7 |
| Strict alignment | |||
| Unfiltered | 11 008 190 | 6 401 927 (4 857 606) | N/A |
| Fastx-Toolkit | 8 263 345 | 7 187 257 (N/A) | — |
| Reaper | 9 355 765 | 8 010 326 (N/A) | — |
| Cutadapt | 9 390 371 | 8 086 428 (N/A) | — |
| EA-Utils | 8 910 356 | 7 757 108 (7 056 242) | — |
| Scythe/Sickle | 9 339 668 | 8 060 612 (6 993 076) | — |
| AdapterRemoval | 9 454 189 | 8 103 596 (7 050 788) | — |
| Trimmomatic SW | 9 355 985 | 8 111 470 (7 068 406) | — |
| Trimmomatic MI | 9 456 124 | 8 748 401 (8 053 230) | — |
Note: Both quality modes are shown for Trimmomatic. Best values are indicated in bold. MI indicates Maximum Information mode, and SW indicates Sliding Window mode.
aTotal reads aligned, and the subset that are aligned as pairs.
bShows wall time, for both serial and parallel execution. See Supplementary Methods for more details.