Table 1.
Comparison between Draft Assemblies Obtained by Different Tools on Simulated Data
| Genome | Assembler | Contigs | Genome Fraction | NGA50 | Misassemblies Extensive + Local | Mismatch Rate | Indel Rate | Time | Memory (GB) |
|---|---|---|---|---|---|---|---|---|---|
| E. coli | Canu | 1 | 99.648 | 4,625,313 | 0 + 0 | 0.86 | 15.85 | 30:18 | 4.16 |
| Flye | 1 | 99.937 | 4,639,833 | 0 + 0 | 0.34 | 25.31 | 5:59 | 12.10 | |
| wtdbg2 | 135 | 96.158 | 107,864 | 4 + 79 | 216.99 | 492.12 | 0:46 | 19.36 | |
| miniasm | 4 | 99.470 | 4,178,447 | 0 + 1 | 52.24 | 646.11 | 0:41 | 2.56 | |
| Minia | 162 | 97.713 | 58,763 | 0 + 0 | 0.26 | 0.00 | 0:26 | 3.04 | |
| SPAdes | 79 | 98.333 | 176,163 | 1 + 2 | 1.69 | 0.11 | 6:56 | 113.92 | |
| hybridSPAdes | 1 | 100.000 | 4,641,652 | 0 + 0 | 6.18 | 0.32 | 8:05 | 113.92 | |
| Unicycler | 1 | 99.997 | 4,641,530 | 0 + 0 | 3.12 | 0.45 | 18:43 | 21.56 | |
| DBG2OLC | 2 | 92.497 | 2,647,379 | 0 + 0 | 0.28 | 30.05 | 4:37 | 1.35 | |
| MaSuRCA | 1 | 99.874 | 4,636,209 | 0 + 4 | 0.56 | 0.19 | 5:21 | 32.52 | |
| Wengan | 1 | 100.000 | 4,641,731 | 0 + 0 | 2.54 | 5.36 | 2:21 | 3.19 | |
| HASLR | 1 | 99.999 | 4,643,699 | 0 + 0 | 2.00 | 42.89 | 0:41 | 3.04 | |
| Yeast | Canu | 21 | 98.831 | 910,628 | 0 + 0 | 3.18 | 25.44 | 44:10 | 5.51 |
| Flye | 19 | 99.418 | 916,686 | 6 + 1 | 11.37 | 49.72 | 9:03 | 19.65 | |
| wtdbg2 | 490 | 92.871 | 77,726 | 24 + 191 | 259.00 | 577.63 | 1:58 | 28.35 | |
| miniasm | 18 | 96.637 | 776,254 | 0 + 0 | 54.28 | 709.35 | 1:49 | 6.63 | |
| Minia | 608 | 94.104 | 39,673 | 0 + 0 | 0.46 | 0.04 | 1:03 | 5.05 | |
| SPAdes | 211 | 95.231 | 151,550 | 0 + 0 | 5.62 | 0.69 | 16:16 | 113.93 | |
| hybridSPAdes | 38 | 97.840 | 797,316 | 2 + 12 | 41.54 | 2.12 | 19:41 | 113.93 | |
| Unicycler | 52 | 97.893 | 799,601 | 0 + 1 | 8.81 | 0.44 | 57:47 | 22.99 | |
| DBG2OLC | 18 | 98.492 | 771,063 | 1 + 0 | 5.9 | 85.95 | 13:29 | 1.21 | |
| MaSuRCA | 17 | 99.476 | 919,651 | 0 + 3 | 5.97 | 0.56 | 15:10 | 32.66 | |
| Wengan | 22 | 97.065 | 796,244 | 0 + 0 | 6.14 | 24.48 | 4:14 | 5.55 | |
| HASLR | 18 | 96.597 | 796,649 | 0 + 0 | 5.39 | 76.63 | 1:52 | 10.48 | |
| C. elegans | Canu | 10 | 99.847 | 13,775,238 | 3 + 1 | 5.88 | 67.73 | 5:15:05 | 13.76 |
| Flye | 16 | 99.798 | 15,266,425 | 8 + 0 | 1.10 | 55.35 | 1:01:26 | 89.50 | |
| wtdbg2 | 4,487 | 95.468 | 81,074 | 194 + 506 | 246.33 | 657.89 | 15:57 | 29.45 | |
| miniasm | 37 | 99.696 | 7,468,924 | 3 + 7 | 68.24 | 864.11 | 20:37 | 19.35 | |
| Minia | 13,546 | 86.788 | 10,047 | 13 + 4 | 0.76 | 0.11 | 6:18 | 8.36 | |
| SPAdes | 3,219 | 94.713 | 58,307 | 30 + 62 | 6.42 | 1.36 | 2:45:34 | 114.80 | |
| hybridSPAdes | 340 | 98.643 | 924,797 | 67 + 197 | 73.26 | 9.14 | 3:11:50 | 114.79 | |
| Unicycler | NA | ||||||||
| DBG2OLC | 16 | 99.692 | 6,732,354 | 10 + 7 | 8.55 | 174.21 | 2:04:23 | 7.99 | |
| MaSuRCA | 18 | 99.609 | 4,614,507 | 34 + 123 | 14.89 | 4.56 | 2:07:41 | 33.76 | |
| Wengan | 46 | 98.917 | 2,042,350 | 53 + 20 | 7.26 | 59.81 | 28:21 | 11.18 | |
| HASLR | 25 | 99.182 | 6,455,832 | 0 + 0 | 14.74 | 230.58 | 10:45 | 22.42 | |
| Human | Canu | 1,461 | 97.279 | 15,045,226 | 854 + 99 | 37.7 | 196.78 | 562:14:04 | 58.72 |
| Flye | NA | ||||||||
| wtdbg2 | 122,438 | 92.735 | 87,595 | 3,436 + 13,041 | 224.02 | 598.87 | 10:25:19 | 190.07 | |
| miniasm | 2,528 | 97.170 | 10,294,834 | 374 + 181 | 71.56 | 775.18 | 110:33:23 | 511.16 | |
| Minia | 593,601 | 80.704 | 4,537 | 1,016 + 16 | 1.55 | 0.13 | 3:29:08 | 8.91 | |
| SPAdes | NA | ||||||||
| hybridSPAdes | NA | ||||||||
| Unicycler | NA | ||||||||
| DBG2OLC | 1,906 | 91.013 | 14,385,033 | 221 + 246 | 8.43 | 201.56 | 81:18:15 | 69.53 | |
| MaSuRCA | NA | ||||||||
| Wengan | 1,776 | 94.617 | 11,216,374 | 185 + 70 | 3.84 | 33.5 | 20:12:12 | 38.08 | |
| HASLR | 897 | 91.213 | 17,025,446 | 2 + 5 | 11.32 | 207.88 | 6:06:43 | 58.55 |
Note: Mismatch and indel rates are reported per 100 kbp. Unicycler crashed on C. elegans dataset due to maximum recursion limit. For the human dataset, Flye, SPAdes, hybridSPAdes, and Unicycler failed due to memory limit and MaSuRCA failed due to a segmentation fault.