Table 3.
Hybrid scaffolding assembly statistics
| Original assembler | Original data type | Original coverage | Approx. PacBio coverage | # Scaffolds | % improvement | Max scaffold size | % improvement | N50 | % improvement | Total bases | Gaps | Median gap size |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Velvet | MiSeq | 75X | 25X | 94 | 38.96% | 789973 | 183.69% | 297566 | 249.55% | 4530346 | 20 | 141 |
| 55X | 86 | 44.16% | 1184298 | 275.38% | 581705 | 487.84% | 4529781 | 15 | 104 | |||
| 110X | 77 | 50.00% | 1107981 | 257.63% | 581889 | 487.99% | 4530783 | 14 | 103 | |||
| Ray | MiSeq | 50X | 25X | 56 | 39.78% | 456422 | 137.07% | 261284 | 235.05% | 4579304 | 1 | 25 |
| 55X | 47 | 49.46% | 768167 | 230.70% | 297488 | 267.62% | 4574295 | 0 | n/a | |||
| 110X | 52 | 44.09% | 456422 | 137.07% | 241297 | 217.07% | 4578631 | 0 | n/a | |||
| Ion | 25X | 25X | 92 | 77.83% | 394228 | 522.34% | 186135 | 930.81% | 4605573 | 307 | 201 | |
| 55X | 90 | 78.31% | 324309 | 429.70% | 179686 | 898.56% | 4579067 | 62 | 127 | |||
| 110X | 83 | 80.00% | 466975 | 618.72% | 201280 | 1006.55% | 4592864 | 69 | 175 | |||
| MIRA | MiSeq | 50X | 25X | 201 | 37.38% | 661174 | 298.02% | 249860 | 516.65% | 4597589 | 9 | 209 |
| 55X | 179 | 44.24% | 716302 | 322.87% | 394266 | 815.24% | 4600672 | 17 | 110 | |||
| 110X | 176 | 45.17% | 759703 | 342.43% | 433542 | 896.45% | 4606800 | 23 | 118 | |||
| Ion | 25X | 25X | 112 | 26.80% | 477985 | 169.86% | 141498 | 132.46% | 4569060 | 7 | 104 | |
| 55X | 105 | 31.37% | 477631 | 169.73% | 149865 | 140.29% | 4569565 | 15 | 120 | |||
| 110X | 93 | 39.22% | 537668 | 191.07% | 200457 | 187.66% | 4571203 | 17 | 230 |