Table 2:
Hybrid and long-read assemblies of Arabidopsis thaliana (Ler-0)
| Number of scaffolds | MAX | N50 | Size (Mb) | Fold | Long Read Coverage | Scaffolder /Assembler | Breakpoints | 1-to-1 identity | % Ref covered | ||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Number | Bases (Mb) | % Error | |||||||||
| 2 384 | 1 551 485 | 320 571 | 119.45 | 1.00 | - | Discovar | 91 | 0.48 | 0.49 | 99.07 | 82.044 |
| 1 577 | 5 305 497 | 1 076 408 | 120.05 | 3.36 | 5X | Opera-LG | 174 | 0.978 | 1.00 | 99.07 | 82.054 |
| 1 368 | 9 953 317 | 2 475 756 | 120.26 | 7.72 | 10X | Opera-LG | 202 | 1.197 | 1.22 | 99.07 | 82.047 |
| 1 249 | 16 906 870 | 4 165 132 | 120.32 | 12.99 | 15X | Opera-LG | 206 | 1.237 | 1.26 | 99.07 | 82.052 |
| 1 179 | 18 032 662 | 4 941 257 | 120.41 | 15.41 | 20X | Opera-LG | 218 | 1.588 | 1.62 | 99.07 | 82.060 |
| 1 103 | 14 710 653 | 4 756 724 | 120.43 | 14.84 | 30X | Opera-LG | 227 | 1.728 | 1.76 | 99.07 | 82.055 |
| 1 049 | 10 003 725 | 4 667 601 | 120.41 | 14.56 | 50X | Opera-LG | 230 | 1.732 | 1.76 | 99.07 | 82.060 |
| 1 345 | 8 867 374 | 1 632 787 | 120.40 | 5.09 | 5X | ScaffM | 195 | 1.620 | 1.65 | 99.07 | 82.058 |
| 1 143 | 8 867 059 | 5 142 417 | 120.65 | 16.04 | 10X | ScaffM | 203 | 1.319 | 1.34 | 99.07 | 82.045 |
| 1 072 | 11 814 750 | 6 165 459 | 120.73 | 19.23 | 15X | ScaffM | 205 | 1.330 | 1.36 | 99.07 | 82.045 |
| 1 020 | 11 873 221 | 6 221 109 | 120.80 | 19.41 | 20X | ScaffM | 207 | 1.477 | 1.50 | 99.07 | 82.039 |
| 958 | 13 946 812 | 7 073 179 | 120.90 | 22.06 | 30X | ScaffM | 209 | 1.651 | 1.68 | 99.07 | 82.042 |
| 923 | 13 957 620 | 6 292 557 | 120.85 | 19.63 | 50X | ScaffM | 210 | 1.712 | 1.74 | 99.07 | 82.041 |
| 1 593 | 5 296 335 | 1 037 785 | 119.96 | 3.24 | 5X | Boss | 179 | 1.171 | 1.19 | 99.07 | 82.061 |
| 1 371 | 13 608 688 | 2 554 739 | 120.17 | 7.97 | 10X | Boss | 200 | 1.335 | 1.36 | 99.07 | 82.054 |
| 1 239 | 13 643 115 | 2 829 628 | 120.22 | 8.83 | 15X | Boss | 207 | 1.189 | 1.21 | 99.07 | 82.061 |
| 1 173 | 7 977 908 | 3 005 451 | 120.23 | 9.38 | 20X | Boss | 212 | 1.564 | 1.59 | 99.07 | 82.060 |
| 1 093 | 9 004 636 | 2 974 378 | 120.28 | 9.28 | 30X | Boss | 219 | 1.575 | 1.60 | 99.07 | 82.057 |
| 1 031 | 11 011 921 | 3 179 270 | 120.29 | 9.92 | 50X | Boss | 229 | 2.162 | 2.20 | 99.07 | 82.050 |
| 1 439 | 447 211 | 80 063 | 89.84 | - | 10X | Canu | 107 | 0.675 | 1.10 | 98.19 | 51.188 |
| 259 | 4 542 617 | 1 170 676 | 118.25 | - | 20X | Canu-p | 201 | 0.969 | 0.99 | 99.06 | 81.907 |
| 258 | 4 543 625 | 1 170 942 | 118.31 | - | 20X | Canu-q | 183 | 0.831 | 0.85 | 99.02 | 81.808 |
| 259 | 4 535 400 | 1 168 180 | 118.05 | - | 20X | Canu | 185 | 1.030 | 1.09 | 98.82 | 78.874 |
| 119 | 15 152 700 | 6 219 401 | 120.67 | - | 50X | Canu | 219 | 1.766 | 1.79 | 99.02 | 82.565 |
| 88 | 15 945 651 | 8 307 845 | 121.45 | - | 150X | Canu | 215 | 1.935 | 1.95 | 99.06 | 82.938 |
Continuity was measured using maximum and N50 contig/scaffold size, where N50 is the contig/scaffold length such that half of the assembly size is obtained by adding contigs/scaffolds sorted in descending order by length. The quality of the assembly was evaluated via a direct comparison against the A. thaliana TAIR10 reference genome using Nucmer [38] and reported using the Gage [26] statistics, which from 1-to-1 alignment evaluates both identity and structural breakpoints (inversions, relocations, and translocations). An optimal assembly has high continuity, low breakpoint errors, high identity, and high coverage of the reference genome. Canu-p and Canu-q are Canu assemblies polished with Pilon [48] and Quiver, respectively. Pilon and Quiver are tools used after a long-read assembly to improve the quality of the consensus sequence. All datasets and commands used for the hybrid assembly of A. thaliana (Ler-0) are detailed in Table 1 and Supplementary Materials 2 and 3.