Table 1.
Benchmarks of GIS20 mock using QUAST
| Assembly | NG50 (bp) | NGA50 (bp) | # all-misassemblies | Mean sequence identity (%) | Genome fraction (%) | # inter-species misassemblies |
|---|---|---|---|---|---|---|
| (A) PE and ONT, all reference genomes. | ||||||
| MetaPlatanus | 757 098 | 171 795 | 201 | 99.9179 | 61.63 | 0 |
| MetaPlatanus w/o closing | 756 452 | 149 303 | 136 | 99.9879 | 59.70 | 0 |
| MetaPlatanus w/o correction | 494 840 | 148 578 | 231 | 99.9375 | 61.76 | 6 |
| metaSPAdes | 234 822 | 73 215 | 528 | 99.8405 | 63.35 | 5 |
| OPERA-MS | 168 587 | 46 454 | 512 | 99.8619 | 60.66 | 5 |
| metaFlye raw | 609 353 | 86 681 | 255 | 99.2566 | 55.28 | 1 |
| metaFlye polished | 610 750 | 90 756 | 171 | 99.9218 | 55.69 | 1 |
| (B) PE and PacBio, all reference genomes. | ||||||
| Assembly | NG50 (bp) | NGA50 (bp) | # all-misassemblies | Mean sequence identity (%) | Genome fraction (%) | # inter-species misassemblies |
| MetaPlatanus | 1 444 699 | 129 682 | 280 | 99.9390 | 69.95 | 0 |
| MetaPlatanus w/o closing | 1 444 050 | 121 228 | 163 | 99.9910 | 68.16 | 2 |
| MetaPlatanus w/o correction | 617 373 | 121 198 | 302 | 99.9507 | 69.89 | 4 |
| metaSPAdes | 374 634 | 112 139 | 219 | 99.8685 | 75.47 | 4 |
| OPERA-MS | 135 973 | 40 414 | 423 | 99.8566 | 71.51 | 13 |
| metaFlye raw | 235 065 | 11 717 | 242 | 99.7181 | 50.04 | 5 |
| metaFlye polished | 235 089 | 13 257 | 256 | 99.9221 | 50.32 | 5 |
| (C) PE and ONT, complete reference genomes only. | ||||||
| Assembly | NG50 (bp) | NGA50 (bp) | # all-misassemblies | Mean sequence identity (%) | Genome fraction (%) | |
| MetaPlatanus | 1 679 878 | 423 879 | 138 | 99.9239 | 67.07 | |
| MetaPlatanus w/o closing | 1 677 738 | 414 037 | 81 | 99.9871 | 65.23 | |
| MetaPlatanus w/o correction | 841 595 | 369 997 | 144 | 99.9477 | 67.17 | |
| metaSPAdes | 421 415 | 163 808 | 420 | 99.8632 | 68.55 | |
| OPERA-MS | 253 089 | 130 701 | 317 | 99.8962 | 66.09 | |
| metaFlye raw | 2 391 293 | 211 481 | 215 | 99.2610 | 62.97 | |
| metaFlye polished | 2 398 268 | 212 079 | 127 | 99.9178 | 63.45 | |
| (D) PE and PacBio, complete reference genomes only. | ||||||
| Assembly | NG50 (bp) | NGA50 (bp) | # all-misassemblies | Mean sequence identity (%) | Genome fraction (%) | |
| MetaPlatanus | 1 870 893 | 401 772 | 178 | 99.9355 | 75.27 | |
| MetaPlatanus w/o closing | 1 870 683 | 401 772 | 88 | 99.9890 | 73.40 | |
| MetaPlatanus w/o correction | 1 051 605 | 349 570 | 216 | 99.9465 | 75.24 | |
| metaSPAdes | 625 209 | 314 514 | 127 | 99.8649 | 81.42 | |
| OPERA-MS | 233 394 | 90 469 | 332 | 99.8426 | 77.13 | |
| metaFlye raw | 2 421 686 | 38 550 | 198 | 99.6941 | 56.46 | |
| metaFlye polished | 2 421 728 | 40 331 | 212 | 99.9126 | 56.80 | |