Table 3. Summary of top-ranking assemblies generated in case study III.
| Organism (Genome Size) | Best Assembly from Each Sequencing Strategy | Assembly Statisticsa | ||
|---|---|---|---|---|
| Scaffold N50 (kb) | Largest Scaffold (kb) | Assembled Fraction of the Reference Genome | ||
| D. melanogaster (137.55 Mb) | ILMN2 | 169.7 | 1,007.9 | 89.1% |
| ILMN8 | 155.0 | 1,007.7 | 91.8% | |
| PACB2 | 5107.5 | 13,108.3 | 99.3% | |
| HYBR2 | 279.3 | 1,536.8 | 89.7% | |
| A. thaliana (119.15 Mb) | ILMN2 | 307.0 | 1,789.4 | 97.3% |
| ILMN8 | 266.6 | 2,533.4 | 98.5% | |
| PACB2 | 2065.7 | 8,552.9 | 99.7% | |
| HYBR2 | 289.3 | 1,412.2 | 97.4% | |
| Pl. falciparum 3D7 (23.29 Mb) | ILMN2 | 28.0 | 146.2 | 96.7% |
| ILMN8 | 222.0 | 729.9 | 98.4% | |
| PACB2 | 282.9 | 1,378.8 | 99.6% | |
| HYBR2 | 15.5 | 91.5 | 97.4% | |
| Pl. falciparum IT (real data) | ILMN2 | 167.1 | 641.7 | >100% |
| ILMN8 | 141.2 | 631.4 | 97.6% | |
| PACB3 | 1574.7 | 3,355.3 | 97.7% | |
| HYBR2 | 198.4 | 602.1 | 92.2% | |
a
The statistics for simulation-based analysis of D. melanogaster, A. thaliana, and Pl. falciparum 3D7 are after correction for assembly errors using the reference genome, as reported by QUAST in GAGE mode. By default, QUAST (in GAGE mode) corrects contigs/scaffolds by breaking them at assembly errors larger than 5 bp. The statistics for real data based analysis of Pl. falciparum IT are calculated from the original de novo assemblies.