Table 2.
Consensus sequence statistics
| Species | Assembler | Input data | Total (Mbp) | Total / geome-size | Scaffold NG50 (kbp) | Scaffold LG50 (#) | Contig NG50 (kbp) | Contig LG50 (#) | % gaps | BUSCO single complete (%) |
|---|---|---|---|---|---|---|---|---|---|---|
| P. polytes | Platanus-allee | PE + 4 MP | 248 | 1.032 | 8,204 | 10 | 157 | 460 | 3.22 | 95.95 |
| PE + 4 MP + PacBio(20 × ) | 247 | 1.028 | 7,784 | 10 | 164 | 438 | 3.18 | 96.19 | ||
| PE + 4 MP + 10X | 248 | 1.031 | 6,621 | 13 | 138 | 516 | 3.08 | 96.40 | ||
| PE + 4 MP + PacBio(20 × ) + 10X | 247 | 1.029 | 7,845 | 11 | 145 | 482 | 3.02 | 96.44 | ||
| Platanus (v1.2.4) | PE + 4 MP | 232 | 0.968 | 5,995 | 15 | 159 | 438 | 1.37 | 96.52 | |
| FALCON-Unzip | PacBio(99 × ) | 261 | 1.088 | 5,196 | 18 | 5,196 | 18 | 0.00 | 89.35 | |
| FALCON-Unzip, Pilon, PH | PacBio(99 × ) + PE | 242 | 1.008 | 5,199 | 18 | 5,199 | 18 | 0.00 | 92.47 | |
| Supernova | 10X | 257 | 1.070 | 329 | 201 | 98 | 638 | 1.75 | 88.00 | |
| B. japonicum | Platanus-allee | PE + 3 MP | 384 | 0.984 | 5,336 | 22 | 48 | 2,149 | 4.40 | 94.07 |
| PE + 3 MP + PacBio(20 × ) | 389 | 0.997 | 7,304 | 16 | 49 | 2,120 | 5.12 | 94.58 | ||
| PE + 3 MP + 10X | 392 | 1.004 | 4,914 | 21 | 34 | 3,104 | 4.52 | 93.87 | ||
| PE + 3 MP + PacBio(20 × ) + 10X | 397 | 1.017 | 5,413 | 17 | 35 | 3,030 | 5.15 | 94.07 | ||
| Platanus (v1.2.4) | PE + MP | 488 | 1.250 | 239 | 414 | 10 | 10,393 | 13.89 | 65.75 | |
| FALCON-Unzip | PacBio(156 × ) | 707 | 1.812 | 4,301 | 32 | 4301 | 32 | 0.00 | 27.91 | |
| FALCON-Unzip, Pilon, PH | PE + PacBio(156 × ) | 406 | 1.042 | 3,259 | 39 | 3,259 | 39 | 0.00 | 84.97 | |
| Supernova | 10X | 662 | 1.697 | 45 | 2271 | 23 | 5,554 | 2.86 | 54.09 | |
| C. elegans | Platanus-allee | PE + 3 MP | 106 | 1.058 | 2,388 | 14 | 63 | 458 | 4.76 | 95.52 |
| PE + 3 MP + PacBio(20 × ) | 107 | 1.065 | 3,316 | 12 | 64 | 456 | 5.13 | 95.11 | ||
| Platanus (v1.2.4) | PE + 3 MP | 102 | 1.016 | 1,848 | 19 | 71 | 364 | 2.30 | 96.64 | |
| FALCON-Unzip | PacBio(192 × ) | 109 | 1.093 | 2,064 | 17 | 2,064 | 17 | 0.00 | 93.18 | |
| FALCON-Unzip, Pilon, PH | PacBio(192 × ) + PE | 103 | 1.029 | 2,064 | 17 | 2,064 | 17 | 0.00 | 94.60 | |
| H. sapiens | Platanus-allee | PE + 4 MP | 2,894 | 0.934 | 3,917 | 230 | 23 | 34,650 | 4.08 | 88.82 |
| PE + 4 MP + PacBio(x20) | 2,995 | 0.966 | 3,717 | 250 | 22 | 36,365 | 6.76 | 86.45 | ||
| PE + 4 MP + 10X | 2,914 | 0.940 | 3,050 | 305 | 25 | 33,967 | 2.46 | 89.34 | ||
| PE + 4 MP + PacBio(20 × ) + 10X | 2,954 | 0.953 | 3,730 | 252 | 24 | 34,583 | 3.66 | 88.66 | ||
| Platanus (v1.2.4) | PE + 4 MP | 2,706 | 0.873 | 13,149 | 65 | 24 | 33,902 | 1.62 | 90.39 | |
| FALCON-Unzip | PacBio(77 × ) | 2,788 | 0.899 | 8,670 | 98 | 8,670 | 98 | 0.00 | 87.97 | |
| FALCON-Unzip, Pilon, PH | PacBio(77 × ) + PE | 2,791 | 0.900 | 8,669 | 98 | 8,669 | 98 | 0.00 | 88.97 | |
| Supernova | 10X | 2,942 | 0.949 | 30,823 | 28 | 147 | 5,954 | 1.42 | 90.33 | |
| Mostovoy et al. 2016 | PE + 1 MP + 10X + Bionano | 2,857 | 0.922 | 30,830 | 34 | 9 | 91,880 | 10.22 | 88.76 |
Statistics were calculated for consensus (pseudo-haploid) sequences whose length ≥ 500 bp. P. polytes, B. japonicum, C. elegans and H. sapiens correspond to a butterfly, am amphioxus, a worm and the human (NA12878), respectively. A bold value indicates the best one for each species. Genome sizes were estimated based on the k-mer frequency information of PEs and GenomeScope26. Total/genome-size, NG50s, and LG50s were calculated based on the estimated haploid genome sizes (P. polytes, 240 Mbp; B. japonicum, 390 Mbp; C. elegans, 100 Mbp; H. sapiens 3.1 Gbp). BUSCO was used to estimate the rate of the non-redundantly constructed single-copy genes in a similar manner for the phased blocks (Table 1). The formats of the results from FALCON-Unzip and Supernova were “primary-contigs” and “pseudohap,” respectively