Table 2. Number of first (or best) alignment reported by various methods on simulated 100-bp data set.
| Rank | 100-bp data set #Correct hits | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Aligner | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | Sum of correct hits |
| BatAlign | 924272 | 7599 | 941 | 728 | 851 | 332 | 182 | 108 | 101 | 63 | 935177 |
| Bowtie2 | 866310 | 8685 | 2833 | 948 | 254 | 110 | 69 | 42 | 23 | 5 | 879279 |
| BWA-SW | 794661 | 7 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 794668 |
| Seqalto | 890336 | 1821 | 515 | 194 | 91 | 44 | 38 | 11 | 3 | 8 | 893061 |
| GEM | 875333 | 10327 | 3533 | 1445 | 638 | 377 | 283 | 193 | 163 | 178 | 892470 |
| BWA-Short | 484558 | 5207 | 1747 | 662 | 211 | 112 | 79 | 48 | 20 | 13 | 492657 |
| BWA-MEM | 912562 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 912562 |