Table 2.
Experiment result on the four real datasets with different read lengths
| Real datasets | Aligner | Sensitivity | Identical base pairs | MEM (Gb) | Runtime |
|---|---|---|---|---|---|
| SRR622458 Illumina-101 bp | Kart | 98.6 | 99 | 12 | 158 |
| Bowtie2 | 97.4 | 99 | 4.5 | 458 | |
| BWA-MEM | 98.8 | 97 | 8.5 | 1157 | |
| Cushaw3 | 99.1 | 98 | 4.8 | 9063 | |
| HPG-Aligner | NA | NA | 31.2 | NA | |
| HISAT2 | 86.0 | 99 | 5.5 | 298 | |
| Subread | 91.2 | 97 | 18.4 | 1362 | |
| SRR826460 Illumina-150 bp | Kart | 99.3 | 149 | 12 | 186 |
| Bowtie2 | 98.4 | 149 | 4.5 | 769 | |
| BWA-MEM | 99.3 | 147 | 8.5 | 1374 | |
| Cushaw3 | 99.3 | 148 | 4.8 | 10736 | |
| HPG-Aligner | 98.3 | 147 | 31.2 | 1204 | |
| HISAT2 | 91.9 | 149 | 5.5 | 371 | |
| Subread | 97.5 | 147 | 18.4 | 2694 | |
| SRR826471 Illumina-250 bp | Kart | 98.6 | 237 | 12 | 395 |
| Bowtie2 | 94.7 | 237 | 4.5 | 1729 | |
| BWA-MEM | 98.6 | 220 | 8.5 | 3027 | |
| Cushaw3 | 98.4 | 232 | 4.6 | 37689 | |
| HPG-Aligner | NA | NA | 27.9 | NA | |
| HISAT2 | 43.9 | 247 | 5.5 | 461 | |
| Subread | NA | NA | 18.4 | NA | |
| M130929 PacBio-7118 bp | Kart | 100.0 | 5152 | 13 | 1811 |
| BWA-MEM | 90.7 | 2953 | 9 | 7338 | |
| LAST | 97.2 | 5022 | 15 | 31295 | |
| BLASR | 97.8 | 5389 | 28.9 | 18682 |