Table 3. Assembly performance comparison on the S. cerevisiae genome (genome size: 12 M bp).
| Cov | Assembler | Time (h) | NG50 | Contigs | NGA50 (454) | Identity (454) | Misass-emblies (454) | NGA50 (PacBio) | Identity (PacBio) | Misass-emblies (PacBio) | Longest | Sum |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 10x | MHAP* | — | — | — | — | — | — | — | — | — | — | — |
| HGAP* | 36.3 | — | 554 | — | 99.68% | 105 | — | 99.77% | 6 | 36,942 | 1,512,911 | |
| CA* | 15.1 | 85,728 | 289 | 68,030 | 97.49% | 134 | 81,451 | 97.46% | 13 | 448,177 | 12,285,888 | |
| PacBioToCA | 173.5 | 19,694 | 898 | 19,378 | 99.88% | 112 | 18,689 | 99.90% | 6 | 221,736 | 10,741,663 | |
| ECTools | 24.5 | 120,126 | 169 | 98,965 | 99.76% | 324 | 109,640 | 99.73% | 29 | 525,820 | 11,785,741 | |
| Falcon* | 1.3 | — | 675 | — | 99.23% | 116 | — | 99.28% | 4 | 36,616 | 4,137,485 | |
| DBG2OLC | 1.7 | 475,890 | 67 | 168,612 | 99.70% | 408 | 355,269 | 99.81% | 46 | 1,174,277 | 11,899,604 | |
| 20x | MHAP* | 17.1 | 241,394 | 87 | 155,221 | 99.70% | 508 | 241,260 | 99.75% | 22 | 490,764 | 12,123,145 |
| HGAP* | 31.1 | 8,578 | 1,210 | 6,908 | 99.85% | 307 | 7,619 | 99.90% | 20 | 86,998 | 8,624,090 | |
| CA* | 42.4 | 371,115 | 165 | 201,649 | 98.83% | 284 | 329,930 | 98.82% | 21 | 680,599 | 13,052,212 | |
| PacBioToCA | 400.9 | 66,974 | 395 | 65,171 | 99.87% | 157 | 65,171 | 99.91% | 7 | 628,280 | 11,487,222 | |
| ECTools | 34.2 | 176,663 | 172 | 109,931 | 99.77% | 565 | 150,351 | 99.74% | 46 | 624,112 | 12,887,799 | |
| Falcon* | 3.5 | 110,083 | 180 | 93,385 | 99.38% | 345 | 110,438 | 99.42% | 15 | 281,041 | 10,583,868 | |
| DBG2OLC | 2.6 | 597,541 | 47 | 172,455 | 99.71% | 440 | 576,287 | 99.88% | 37 | 1,085,773 | 12,476,994 | |
| 40x | MHAP* | 36.6 | 614,363 | 65 | 243,012 | 99.91% | 598 | 589,044 | 99.94% | 24 | 1,090,578 | 12,356,826 |
| HGAP* | 36.2 | 211,631 | 93 | 198,387 | 99.94% | 528 | 348,754 | 99.99% | 30 | 796,762 | 12,387,287 | |
| CA* | 115.2 | 365,912 | 114 | 160,867 | 99.66% | 358 | 377,360 | 99.60% | 11 | 769,189 | 15,171,228 | |
| PacBioToCA | 621.7 | 96,817 | 371 | 96,476 | 99.87% | 178 | 94,480 | 99.91% | 6 | 742,046 | 11,700,172 | |
| ECTools | 55.8 | 255,956 | 271 | 166,945 | 99.79% | 891 | 214,377 | 99.76% | 64 | 714,196 | 14,481,947 | |
| Falcon* | 11.2 | 614,509 | 58 | 247,745 | 99.72% | 336 | 555,886 | 99.74% | 10 | 1,069,920 | 12,116,235 | |
| DBG2OLC | 4.2 | 672,955 | 28 | 238,683 | 99.87% | 431 | 544,679 | 99.90% | 36 | 1,086,380 | 12,149,997 | |
| 80x | MHAP* | 13.5 | 751,122 | 43 | 248,079 | 99.91% | 526 | 745,563 | 99.95% | 10 | 1,537,433 | 12,350,704 |
| HGAP* | 46.5 | 818,775 | 33 | 248,655 | 99.95% | 534 | 678,552 | 99.99% | 23 | 1,545,906 | 12,621,393 | |
| CA* | 236.0 | 430,552 | 75 | 201,397 | 99.80% | 319 | 397,774 | 99.74% | 12 | 984,295 | 16,571,250 | |
| PacBioToCA | 274.3 | 64,967 | 364 | 63,651 | 99.88% | 45 | 62,268 | 99.91% | 10 | 233,799 | 11,651,218 | |
| ECTools | 100.9 | 247,871 | 382 | 154,348 | 99.79% | 1,470 | 164,839 | 99.76% | 101 | 881,635 | 15,925,328 | |
| Falcon* | 34.7 | 810,136 | 99 | 247,480 | 99.81% | 437 | 810,134 | 99.82% | 24 | 1,537,463 | 12,681,860 | |
| DBG2OLC | 8.1 | 678,365 | 29 | 204065 | 99.92% | 426 | 574,476 | 99.95% | 35 | 1,089,897 | 12,209,592 |
*Assemblers that use only 3GS data.