Table 2.
The assembly contiguity (scaffold NG50 and NGA50) and correctness (number of misassemblies) metrics with and without correction using Tigmint prior to scaffolding with ARCS
| Sample | Assembly | NG50 (Mbp) | NGA50 (Mbp) | Misass. | Reduction |
|---|---|---|---|---|---|
| HG004 | ABySS | 3.65 | 3.09 | 790 | NA |
| ABySS+Tigmint | 3.47 | 3.09 | 574 | 216 (27.3%) | |
| ABySS+ARCS | 9.91 | 7.86 | 823 | NA | |
| ABySS+Tigmint+ARCS | 26.39 | 16.43 | 641 | 182 (22.1%) | |
| HG004 | DISCO+ABySS | 10.55 | 9.04 | 701 | NA |
| DISCO+ABySS+Tigmint | 10.16 | 9.04 | 666 | 35 (5.0%) | |
| DISCO+ABySS+ARCS | 29.20 | 17.05 | 829 | NA | |
| DISCO+ABySS+Tigmint+ARCS | 35.31 | 23.68 | 804 | 25 (3.0%) | |
| HG004 | DISCO+BESST | 7.01 | 6.14 | 568 | NA |
| DISCO+BESST+Tigmint | 6.77 | 6.14 | 493 | 75 (13.2%) | |
| DISCO+BESST+ARCS | 27.64 | 15.14 | 672 | NA | |
| DISCO+BESST+Tigmint+ARCS | 33.43 | 19.40 | 603 | 69 (10.3%) | |
| HG004 | Supernova | 38.48 | 12.65 | 1005 | NA |
| Supernova+Tigmint | 17.72 | 11.43 | 923 | 82 (8.2%) | |
| Supernova+ARCS | 39.63 | 13.24 | 1052 | NA | |
| Supernova+Tigmint+ARCS | 27.35 | 12.60 | 998 | 54 (5.1%) | |
| HG004 | Falcon | 4.56 | 4.21 | 3640 | NA |
| Falcon+Tigmint | 4.45 | 4.21 | 3444 | 196 (5.4%) | |
| Falcon+ARCS | 18.14 | 9.71 | 3,801 | NA | |
| Falcon+Tigmint+ARCS | 22.52 | 11.97 | 3,574 | 227 (6.0%) | |
| NA12878 | Canu | 7.06 | 5.40 | 1688 | NA |
| Canu+Tigmint | 6.87 | 5.38 | 1600 | 88 (5.2%) | |
| Canu+ARCS | 19.70 | 10.12 | 1736 | NA | |
| Canu+Tigmint+ARCS | 22.01 | 10.85 | 1,626 | 110 (6.3%) | |
| Simulated | ABySS | 9.00 | 8.28 | 272 | NA |
| ABySS+Tigmint | 8.61 | 8.28 | 217 | 55 (20.2%) | |
| ABySS+ARCS | 23.37 | 17.09 | 365 | NA | |
| ABySS+Tigmint+ARCS | 30.24 | 24.98 | 320 | 45 (12.3%) |
ABySS and DISCOVARdenovo are assemblies of Illumina sequencing. Supernova is an assembly of linked read sequencing. Falcon is an assembly of PacBio sequencing. Canu is an assembly Oxford Nanopore sequencing. Data simulated with LRSim is assembled with ABySS