Table 1 Performance of reference-assisted assembly tools
From: GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes
| Â | S. pyogenes A20 | H. pylori G27 | V. cholerae H1 chr1 |
|---|---|---|---|
Ref complete genome, Mb | |||
| Â | 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 |