Table 3.
Results of strict and tolerant BWA alignments of the raw data and trimmed data from each tool (using both quality modes for Trimmomatic) from both datasets
| Dataset | Strict alignmentsa | Tolerant alignmentsb |
|---|---|---|
| Dataset 1 | ||
| Unfiltered | 7 834 544 | 8 750 851 |
| Fastx-Toolkit | 7 187 257 | 7 894 580 |
| Reaper | 8 010 326 | 8 894 757 |
| Cutadapt | 8 086 428 | 8 968 519 |
| EA-Utils | 8 059 850 | 8 896 724 |
| Scythe/Sickle | 8 755 676 | 9 076 936 |
| AdapterRemoval | 8 810 051 | 9 108 691 |
| Trimmomatic SW | 8 810 063 | 9 110 831 |
| Trimmomatic MI | 9 056 403 | 9 145 423 |
| Dataset 2 | ||
| Unfiltered | 11 592 | 60 010 |
| AdapterRemoval | 513 133 | 574 973 |
| Fastx-Toolkit | 525 519 | 550 695 |
| EA-Utils | 538 472 | 588 046 |
| Scythe/Sickle | 567 976 | 588 135 |
| Cutadapt | 568 044 | 613 089 |
| Trimmomatic SW | 590 729 | 628 867 |
| Trimmomatic MI | 634 779 | 639 740 |
Note: Best values are indicated in bold. MI indicates Maximum Information mode, and SW indicates Sliding Window mode.
aReads aligned, zero mismatches permitted.
bReads aligned, one mismatch allowed.