Table 4.
Relevant assembly and BUSCO statistics for the unpolished and polished assemblies of the rooibos genome generated using the five long-read assembly programs: Flye, Canu, Raven, Redbean and NextDenovo.
| Assembly Parameters | Unpolished | Racon_Long | Medaka | Racon_Short | Nextpolish | |
|---|---|---|---|---|---|---|
| Flye | Number of contigs | 33,346 | 32,286 | 32,393 | 31,921 | 32,392 |
| Largest contig (bp) | 921,299 | 925,383 | 928,488 | 926,118 | 925,075 | |
| Total length (Mbp) | 1118.5 | 1107.2 | 1112.5 | 1107.4 | 1110.7 | |
| N50 length (bp) | 77,709 | 78,172 | 78,358 | 78,512 | 78,176 | |
| Complete BUSCOs (%) | 97.3 | 96.5 | 98.0 | 99.2 | 99.2 | |
| Complete single BUSCOs (%) | 65.9 | 71.8 | 70.2 | 65.5 | 64.3 | |
| Complete duplicated BUSCOs (%) | 31.4 | 24.7 | 27.8 | 33.7 | 34.9 | |
| Fragmented BUSCOs (%) | 2.4 | 2.7 | 1.6 | 0.8 | 0.8 | |
| Missing BUSCOs (%) | 0.3 | 0.8 | 0.4 | 0.0 | 0.0 | |
| Canu | Number of contigs | 33,477 | 33,351 | 33,357 | 33,320 | 33,356 |
| Largest contig (bp) | 434,840 | 443,413 | 444,838 | 443,863 | 443,487 | |
| Total length (Mbp) | 949.0 | 965.0 | 970.8 | 968.1 | 969.1 | |
| N50 length (bp) | 40,175 | 41,134 | 41,324 | 41,225 | 41,247 | |
| Complete BUSCOs (%) | 96.1 | 98.8 | 99.2 | 99.6 | 99.6 | |
| Complete single BUSCOs (%) | 71.4 | 72.5 | 72.5 | 57.6 | 56.9 | |
| Complete duplicated BUSCOs (%) | 24.7 | 26.3 | 26.7 | 42.0 | 42.7 | |
| Fragmented BUSCOs (%) | 2.4 | 0.0 | 0.4 | 0.0 | 0.0 | |
| Missing BUSCOs (%) | 1.5 | 1.2 | 0.4 | 0.4 | 0.4 | |
| Raven | Number of contigs | 11,675 | 11,674 | 11,674 | 11,672 | 11,674 |
| Largest contig (bp) | 760,847 | 765,889 | 767,221 | 765,347 | 764,913 | |
| Total length (Mbp) | 905.6 | 909.8 | 915.2 | 912.6 | 913.1 | |
| N50 length (bp) | 99,352 | 99,903 | 100,315 | 100,069 | 100,060 | |
| Complete BUSCOs (%) | 96.9 | 95.7 | 96.9 | 97.6 | 98.0 | |
| Complete single BUSCOs (%) | 79.6 | 76.9 | 79.6 | 69.0 | 69.4 | |
| Complete duplicated BUSCOs (%) | 17.3 | 18.8 | 17.3 | 28.6 | 28.6 | |
| Fragmented BUSCOs (%) | 1.2 | 2.4 | 1.2 | 0.8 | 0.8 | |
| Missing BUSCOs (%) | 1.9 | 1.9 | 1.9 | 1.6 | 1.2 | |
| Redbean | Number of contigs | 16,753 | 16,347 | 16,350 | 16,275 | 16,350 |
| Largest contig (bp) | 1,686,036 | 1,739,027 | 1,738,674 | 1,734,655 | 1,734,062 | |
| Total length (Mbp) | 962.0 | 993.5 | 996.8 | 994.0 | 995.1 | |
| N50 length (bp) | 142,771 | 148,572 | 148,398 | 148,157 | 148,018 | |
| Complete BUSCOs (%) | 83.9 | 96.5 | 98.8 | 99.2 | 99.2 | |
| Complete single BUSCOs (%) | 80.4 | 82.4 | 85.9 | 74.9 | 75.3 | |
| Complete duplicated BUSCOs (%) | 3.5 | 14.1 | 12.9 | 24.3 | 23.9 | |
| Fragmented BUSCOs (%) | 8.6 | 2.7 | 0.4 | 0.4 | 0.4 | |
| Missing BUSCOs (%) | 7.5 | 0.8 | 0.8 | 0.4 | 0.4 | |
| NextDenovo | Number of contigs | 5431 | 5431 | 5431 | 5431 | 5431 |
| Largest contig (bp) | 3,406,093 | 3,359,923 | 3,371,738 | 3,361,759 | 3,361,805 | |
| Total length (Mbp) | 824.2 | 817.1 | 820.9 | 818.6 | 818.9 | |
| N50 length (bp) | 218,190 | 217,600 | 218,885 | 218,094 | 218,285 | |
| Complete BUSCOs (%) | 90.2 | 92.1 | 93.7 | 94.5 | 94.5 | |
| Complete single BUSCOs (%) | 72.9 | 72.5 | 76.1 | 69.8 | 69.8 | |
| Complete duplicated BUSCOs (%) | 17.3 | 19.6 | 17.6 | 24.7 | 24.7 | |
| Fragmented BUSCOs (%) | 3.1 | 1.2 | 0.4 | 0.4 | 0.4 | |
| Missing BUSCOs (%) | 6.7 | 6.7 | 5.9 | 5.1 | 5.1 |