Table 2.
Benchmark Evaluation of Msuite and Current Software
| Msuite (4-Letter Mode) | Msuite (3-Letter Mode) | Bismark | BWA-metha | |
|---|---|---|---|---|
| 1 Million paired-end 100-bp reads | ||||
| Mapping efficiency (%) | 96.19 | 95.75 | 95.79 | 95.58 |
| Accuracy (%) | 99.94 | 99.95 | 99.93 | 99.96 |
| Running time (s) | 119.45 | 195.80 | 236.37 | 155.14 |
| Peak memory (Gb) | 3.74 | 3.74 | 40.21 | 12.52 |
| 1 Million paired-end 36-bp reads | ||||
| Mapping efficiency (%) | 92.46 | 91.62 | 91.71 | 91.46 |
| Accuracy (%) | 99.79 | 99.63 | 99.65 | 99.67 |
| Running time (s) | 126.60 | 173.84 | 164.80 | 283.55 |
| Peak memory (Gb) | 3.77 | 3.78 | 40.16 | 22.52 |
| 1 Million paired-end 36-bp reads originating from CT/GA ≥ 70% regions | ||||
| Mapping efficiency (%) | 79.67 | 67.14 | 68.39 | 76.31 |
| Accuracy (%) | 99.78 | 99.03 | 98.94 | 92.06 |
| Running time (s) | 120.30 | 307.00 | 294.80 | 360.80 |
| 1 Million paired-end 36-bp reads originating from CT/GA ≥ 80% regions | ||||
| Mapping efficiency (%) | 73.53 | 53.14 | 54.60 | 65.85 |
| Accuracy (%) | 99.81 | 98.38 | 98.19 | 86.91 |
| Running time (s) | 112.60 | 375.00 | 366.00 | 469.70 |
Eight threads were used for benchmark testing, and the data were simulated following the TAPS protocol.
a
For BWA-meth, alignments with a score of 0 were discarded due to abnormally high error rate.