Table 1.
Performance of reference-assisted assembly tools
| S. pyogenes A20 | H. pylori G27 | V. cholerae H1 chr1 | |
|---|---|---|---|
| Ref complete genome, Mb | |||
| 1.85 | 1.67 | 3.08 | |
| Original assemblies | |||
| Number (>300 bp) | 38 | 40 | 41 |
| N50, kb | 124 | 134 | 236 |
| Final scaffolds | |||
| GAAP | 1 | 1 | 1 |
| AlignGraph | 11 | 7 | 15 |
| Ragout | 1 | 1 | 1 |
| MeDuSa | 1 | 1 | 1 |
| Coverage, recovered % (falsely located %) | |||
| GAAP | 98.65 (0.15) | 98.57 (0.06) | 97.85 (0) |
| AlignGraph | 81.93 (8.78) | 61.75 (0) | 79.13 (0) |
| Ragout | 97.35 (17.7) | 98.28 (0.02) | 98.05 (0) |
| MeDuSa | 98.2 (19.7) | 98.95 (0.10) | 98.19 (11.15) |
| Errors | |||
| GAAP | 19 | 5 | 8 |
| AlignGraph | 3 | 2 | 1 |
| Ragout | 6 | 5 | 5 |
| MeDuSa | 9 | 11 | 14 |
| Corrected N50, kb | |||
| GAAP | 273 | 277 | 2,026 |
| AlignGraph | 124 | 138 | 351 |
| Ragout | 103,6 | 1,121 | 1,323 |
| MeDuSa | 252 | 207 | 245 |