Table 3:
Hybrid and long-read assemblies of NA12878
| Discovar | Dfs | 10X | Dovetail | Canu-p | MaSuRCA | ||
|---|---|---|---|---|---|---|---|
| Assembly statistics | Number | 37 393 | 7 323 | 9 926 | 9 463 | 2 337 | 4 885 |
| Min. | 2 000 | 2 000 | 2 000 | 2 000 | 2 981 | 4 103 | |
| Max. | 1 380 479 | 30 548 185 | 69 726 354 | 95 295 052 | 50 410 306 | 9 066 374 | |
| N50 | 202 174 | 6 445 123 | 16 305 019 | 24 472 662 | 7 667 013 | 1 695 766 | |
| Size | 2 794 627 041 | 2 884 349 664 | 2 835 096 130 | 2 800 321 128 | 2 866 880 913 | 2 849 443 591 | |
| Long-read coverage | - | 7X | - | - | 35X | 7X | |
| 1-to-1 alignments | |||||||
| Length | 2 793 980 166 | 2 797 898 328 | 2 778 947 064 | 2 799 630 879 | 2 811 439 829 | 2 845 550 340 | |
| Identity | 99.8 | 99.8 | 99.79 | 99.8 | 99.28 | 99.67 | |
| % Ref covered | 90.16 | 90.29 | 89.68 | 90.35 | 90.73 | 91.83 | |
| Breakpoints | |||||||
| Relocations | Number | 120 | 1 151 | 688 | 997 | 501 | 374 |
| Bases (Mb) | 0.361 | 5.604 | 4.810 | 0.582 | 2.281 | 2.071 | |
| Translocations | Number | 373 | 1 856 | 883 | 976 | 1 082 | 941 |
| Bases (Mb) | 4.840 | 11.279 | 7.838 | 6.576 | 13.781 | 13.933 | |
| Inversions | Number | 53 | 768 | 871 | 2,813 | 299 | 240 |
| Bases (Mb) | 0.151 | 3.886 | 7.273 | 0.736 | 2.903 | 3.008 | |
| Total | Number | 546 | 3 775 | 2 442 | 4 786 | 1 882 | 1 555 |
| Bases (Mb) | 5.353 | 20.769 | 19.921 | 7.894 | 18.964 | 19.012 | |
| %1-to-1 | 0.192 | 0.742 | 0.717 | 0.282 | 0.675 | 0.668 | |
Assembly statistics: Number - number of contigs/scaffolds assembled; Max/Min - the maximum/minimum contig/scaffold size in base pairs; N50 - contig/scaffold length such that half of the assembly size is obtained by adding contigs/scaffolds sorted in descending order by length; size - total size of the assembly in base pairs; 1-to-1 alignments: length - total length of nonrepetitive alignments between the assembly and GRCh38.p10 detected by Nucmer; identity - average identity between the assembly and GRCh38.p10 computed from the 1-to-1 alignments; %Ref covered - percentage of the GRCh38.p10 that is covered by 1-to-1 alignments where the length of the reference was set to 3.1 Gb; Breakpoints - structural errors were obtained from 1-to-1 alignments and reported using the Gage metrics (relocations, translocations, and inversions); number - counts the number of breakpoints by sort; bases (Mb) - adds the number of bases involved in breakpoints extracted from the Dnadiff report (qdiff file) in mega bases; %1-to-1 - percentage of structural errors with respect to the total 1-to-1 alignment length. Public NA12878 assemblies were downloaded and used for validation and comparisons against the DFS hybrid assembly pipeline.