Table 3:
Improved assemblies in the MHC region by TGS-GapCloser
| Statistics | MaSuRCA + SLR-superscaffolder + TGS-GapCloser | Mercedes + SLR-superscaffolder + TGS-GapCloser | Supernova + TGS-GapCloser | Reference [33] | ||||
|---|---|---|---|---|---|---|---|---|
| Draft | Updated | Draft | Updated | Draft | Updated | Rel3 | Rel5 | |
| No. of scaffolds (>1 kb) | 2 | 2 | 3 | 3 | 1 | 1 | – | – |
| No. of scaftigs/contigs (>1 kb) | 339 | 31 | 271 | 26 | 76 | 12 | 7 | 1 |
| Non-N bases (bp) | 5,293,785 | 5,907,069 | 4,134,156 | 5,445,373 | 5,831,980 | 5,988,090 | 5,739,339 | 5,628,041 |
| No. of gaps | 343 | 31 | 268 | 23 | 81 | 16 | – | – |
| Scaffold NG50 (bp) | 3,400,000 | 3,400,000 | 4,400,000 | 4,400,000 | 6,000,000 | 6,000,000 | – | – |
| Scaffold NGA50 (bp) | 232,462 | 396,537 | 182,662 | 429,613 | 649,591 | 534,616 | – | – |
| Scaftig/contig NG50 (bp) | 17,483 | 324,807 | 12,244 | 450,213 | 110,320 | 980,326 | 3,007,673 | 5,628,041 |
| Scaftig/contig NGA50 (bp) | 16,630 | 199,405 | 11,901 | 321,624 | 94,556 | 380,102 | 49,485 | 52,555 |
| Genome fraction (%) | 82.801 | 92.623 | 67.869 | 85.609 | 93.887 | 95.292 | 62.521 | 59.855 |
| No. of misassemblies | 11 | 25 | 13 | 22 | 15 | 17 | 20 | 53 |
| No. of local misassemblies | 34 | 101 | 11 | 122 | 29 | 42 | 546 | 484 |
The statistical results were generated by QUAST. Note that QUAST accepts <10 continuous N's in the scaftig/contig.