Table 1. Assembly Statistics and Run-Time Statistics by Assembly and Postprocessing.
| Assembler | k CPU Hours | Memory (GB) | N50 | L50 | Total Size | Largest Contig | Total Contigs | Illumina Mapping Rate (%) | Qualimap Discrepancy Rate | % Complete BUSCO |
|---|---|---|---|---|---|---|---|---|---|---|
| Raw | ||||||||||
| Canu | 80.42 | 199.87 | 1.48 | 169 | 922.94 | 9.63 | 2010 | 98.52 | 3.74 | 26.46 |
| SMARTdenovo | 0.72 | 55.60 | 1.03 | 271 | 929.99 | 5.68 | 1901 | 98.65 | 4.22 | 26.74 |
| Miniasm | 1.86 | 51.93 | 1.69 | 158 | 956.29 | 9.28 | 2704 | 95.53 | 9.11 | 0.21 |
| Canu-SMARTdenovo | 10.68 | 131.32 | 2.45 | 106 | 889.92 | 12.32 | 899 | 98.73 | 3.68 | 29.1 |
| Pilon Polished 5x | ||||||||||
| Canu | – | – | 1.55 | 169 | 961.83 | 10.01 | 2010 | 98.95 | 0.82 | 96.46 |
| SMARTdenovo | – | – | 1.06 | 270 | 955.31 | 5.84 | 1901 | 98.99 | 0.91 | 96.11 |
| Miniasm | – | – | 1.75 | 156 | 977.78 | 9.49 | 2704 | 98.24 | 2.48 | 85.69 |
| Canu-SMARTdenovo | – | – | 2.52 | 106 | 915.60 | 12.72 | 899 | 98.98 | 0.85 | 96.46 |
All sequence lengths are in megabases. –, CPU and memory resources were not tracked for polishing. See Supplemental Data Set 1 for additional polishing data.