Table 4.
Summary of the Assemblies of Four Simulated Datasets
| LC | ||||||||
|---|---|---|---|---|---|---|---|---|
| Assembler | Assembly size (%) | Num | LLC (bp) | N50 (bp) | CorrN50 (bp) | URB (%) | UAB (%) | F-accuracy |
| DIME-cap3 | 95.6 | 18437 | 3795 | 721 | 720 | 26.8 | 23.4 | 0.75 |
| DIME-genovo | 127.9 | 19406 | 42360 | 810 | 809 | 9.5 | 29.2 | 0.81 |
| Cap3 | 66.3 | 13568 | 2588 | 688 | 687 | 50.3 | 25.2 | 0.62 |
| Genovo | 1.32 | 20317 | 28455 | 810 | 805 | 11.1 | 32.3 | 0.78 |
| MetaVelvet | 12.2 | 2684 | 1810 | 658 | 656 | 88.7 | 7.6 | 0.52 |
| SOAPdenovo | 17.1 | 3620 | 1380 | 721 | 718 | 84.7 | 10.8 | 0.52 |
| SPAdes | 67.8 | 5093 | 3795 | 1014 | 918 | 38.5 | 9.3 | 0.76 |
| MC | ||||||||
|---|---|---|---|---|---|---|---|---|
| DIME-cap3 | 58.6 | 12960 | 2290 | 671 | 669 | 46.1 | 8.0 | 0.73 |
| DIME-genovo | 150.0 | 30704 | 5451 | 725 | 718 | 20.7 | 47.4 | 0.66 |
| Cap3 | 25.2 | 5665 | 2842 | 660 | 658 | 77.1 | 8.8 | 0.57 |
| Genovo | 157.7 | 32006 | 4211 | 728 | 717 | 24.6 | 52.2 | 0.62 |
| MetaVelvet | 17.2 | 3878 | 1356 | 664 | 662 | 84.4 | 9.3 | 0.53 |
| SOAPdenovo | 21.7 | 5375 | 1667 | 707 | 700 | 78.5 | 1.2 | 0.60 |
| SPAdes | 55.6 | 7484 | 5522 | 847 | 747 | 63.1 | 33.6 | 0.52 |
| HC | ||||||||
|---|---|---|---|---|---|---|---|---|
| DIME-cap3 | 57.3 | 11336 | 2338 | 676 | 675 | 45.3 | 4.5 | 0.75 |
| DIME-genovo | 163.7 | 30742 | 4247 | 711 | 704 | 15.2 | 48.2 | 0.68 |
| Cap3 | 24.5 | 4901 | 1716 | 669 | 667 | 77.3 | 7.7 | 0.57 |
| Genovo | 171.4 | 31847 | 4541 | 717 | 703 | 16.0 | 51.0 | 0.66 |
| MetaVelvet | 13.2 | 2684 | 1810 | 658 | 656 | 87.7 | 7.6 | 0.52 |
| SOAPdenovo | 29.7 | 5612 | 1312 | 709 | 706 | 73.6 | 11.4 | 0.57 |
| SPAdes | 45.9 | 5863 | 5425 | 898 | 805 | 68.8 | 32.1 | 0.49 |
| HCh | ||||||||
|---|---|---|---|---|---|---|---|---|
| DIME-cap3 | 81.5 | 362658 | 5096 | 735 | 733 | 33.7 | 18.6 | 0.74 |
| DIME-genovo | 98.8 | 308472 | 36761 | 1052 | 1045 | 15.9 | 14.9 | 0.85 |
| Cap3 | 5.0 | 22852 | 4169 | 718 | 717 | 95.6 | 11.1 | 0.47 |
| Genovo | NA | NA | NA | NA | NA | NA | NA | NA |
| MetaVelvet | 10.6 | 54678 | 2526 | 637 | 637 | 89.8 | 4.8 | 0.53 |
| SOAPdenovo | 26.1 | 137401 | 1603 | 635 | 634 | 76.7 | 11.2 | 0.56 |
| SPAdes | 75.5 | 142296 | 37059 | 1200 | 1103 | 33.9 | 12.4 | 0.77 |
Only contigs of length ≥500 contributed to the statistics.
The value in bold indicates that the assembler obtained the highest F-accuracy.