Table 2 Comparison of VAliBS, Bismark, BS-Seeker2, and BSMAP on simulation data
single end | VAliBS | BS-Seeker2 | Bismark | BSMAP | ||
bowtie2 | Bowtie2 | Bowtie | Bowtie2 | Bowtie | ||
Simulation: error-free | ||||||
map | 92.80% | 91.50% | 91.65% | 87.78% | 91.65% | 91.81% |
c-map | 92.09% | 91.50% | 91.65% | 87.78% | 91.65% | 91.81% |
Simulation: error-containing | ||||||
map | 92.67% | 90.51% | 91.69% | 86.90% | 91.64% | 91.90% |
c-map | 91.23% | 90.26% | 91.59% | 86.79% | 91.46% | 91.82% |
paired end | VAliBS | BS-Seeker2 | Bismark | BSMAP | ||
Bowtie2 | Bowtie2 | Bowtie | Bowtie2 | Bowtie | ||
Simulation: error-free | ||||||
map | 92.79% | 78.02% | 78.29% | 72.51% | 78.08% | 78.63% |
c-map | 92.08% | 78.02% | 78.29% | 72.51% | 78.08% | 78.49% |
Simulation: error-containing | ||||||
map | 94.24% | 78.42% | 78.72% | 71.36% | 78.17% | 79.10% |
c-map | 92.64% | 77.07% | 77.95% | 71.08% | 77.25% | 78.16% |