Table 1.
Comparisons of contig assembly accuracy for authentic data sets from the assembly of contigs from green sulfur bacterial genomes using PGA, PGA-extended, BLAST-end, Projector2 and OSLay
| Genomesa | Contigs | Method | Reference Ctep | Reference Cpha | Reference Plut | 2 or 3 Refs | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| Best | Average | Best | Average | Best | Average | Best | Average | |||
| Clim | 37 | PGA | 0.324 | 0.276 ± 0.040 | 0.405 | 0.373 ± 0.032 | 0.378 | 0.346 ± 0.026 | 0.514b | 0.443 ± 0.040b |
| PGA-ext.e | 0.514 | NA | 0.541 | NA | 0.568 | NA | NA | Na | ||
| BLAST-end | 0.108 | NA | 0.135 | NA | 0.135 | NA | NA | NA | ||
| Projector2 | 0.189 | NA | 0.189 | NA | 0.162 | NA | NA | NA | ||
| OSLay | 0.135 | NA | 0.162 | NA | 0.108 | NA | NA | NA | ||
| Cvib | 26 | PGA | 0.385 | 0.331 ± 0.031 | 0.462 | 0.454 ± 0.015 | 0.769 | 0.738 ± 0.015 | 0.731c | 0.731 ± 0.000c |
| PGA-ext.e | 0.577 | NA | 0.731 | NA | 0.885 | NA | NA | NA | ||
| BLAST-end | 0.115 | NA | 0.385 | NA | 0.538 | NA | NA | NA | ||
| Projector2 | 0.231 | NA | 0.308 | NA | 0.577 | NA | NA | NA | ||
| OSLay | 0.000 | NA | 0.154 | NA | 0.423 | NA | NA | NA | ||
| Cpar | 58 | PGA | 0.690 | 0.679 ± 0.014 | 0.431 | 0.400 ± 0.020 | 0.586 | 0.559 ± 0.018 | 0.741d | 0.738 ± 0.007d |
| PGA-ext.e | 0.914 | NA | 0.621 | NA | 0.724 | NA | NA | NA | ||
| BLAST-end | 0.534 | NA | 0.190 | NA | 0.172 | NA | NA | NA | ||
| Projector2 | 0.224 | NA | 0.121 | NA | 0.155 | NA | NA | NA | ||
| OSLay | 0.534 | NA | 0.052 | NA | 0.103 | NA | NA | NA | ||
aAssembly of contigs of C. limicola (Clim), C. vibrioforme (Cvib) and C. parvum (Cpar) contigs.
bChlorobium tepidum (Ctep), C. phaeobacteriodes (Cpha) and P. luteolum (Plut) were used as the reference genomes.
cChlorobium phaeobacteriodes (Cpha) and P. luteolum (Plut) were used as the reference genomes.
dChlorobium tepidum (Ctep) and P. luteolum (Plut) were used as the reference genomes.
eThe corresponding value indicates the overall success rate for gap closure attained using the four best predictions from the PGA-extended method.
NA, not applicable.