Table 2 The summary of draft assemblies of E. coli, S. cerevisiae, A. thaliana, O. sativa, S. pennellii, Z. mays and H. sapiens
From: LRScaf: improving draft genomes using long noisy reads
Species | Method/Source | Sum | NG50 | NGA50 | Longest | Misassemblies (#) | BUSCO (Complete) |
|---|---|---|---|---|---|---|---|
E. coli | SOAPdenovo2 | 4.6 Mbp | 25.2 kbp | 25.2 kbp | 91.7 kbp | 0 | 97.3% |
SPAdes | 4.6 Mbp | 112.4 kbp | 105.6 kbp | 265.2 kbp | 2 | 98.6% | |
ABySS a | 5.2 Mbp | 179.7 kbp | 146.9 kbp | 358.7 kbp | 5 | 98.6% | |
SparseAssembler b | 4.4 Mbp | 3.0 kbp | 3.0 kbp | 14.9 kbp | 2 | 64.9% | |
S. cerevisiae | SOAPdenovo2 | 12.1 Mbp | 18.7 kbp | 18.6 kbp | 146.7 kbp | 3 | 96.2% |
SPAdes | 11.8 Mbp | 104.1 kbp | 85.7 kbp | 451.4 kbp | 22 | 97.2% | |
Celera Assembly a | 14.9 Mbp | 58.8 kbp | 54.7 kbp | 257.3 kbp | 19 | 98.7% | |
A. thaliana (KBS-Mac-74) | DISCOVAR | 117.9 Mbp | 323.0 kbp | 314.6 kbp | 2.5 Mbp | 67 | 98.5% |
MaSuRCA | 119. 5 Mbp | 413.2 kbp | 356.5 kbp | 1.7 Mbp | 145 | 98.3% | |
Platanus | 113.0 Mbp | 145.5 kbp | 143.7 kbp | 800.8 kbp | 31 | 98.3% | |
SOAPdenovo2 | 115.1 Mbp | 236.7 kbp | 227.0 kbp | 1.5 Mbp | 39 | 98.3% | |
SparseAssembler | 93.0 Mbp | 12.8 kbp | 12.7 kbp | 114.5 kbp | 1 | 94.7% | |
A. thaliana (ler-0) | SparseAssembler b | 74.7 Mbp | 4.4 kbp | 4.2 kbp | 35.8 kbp | 90 | 74.6% |
O. sativa | DISCOVAR | 313.8 Mbp | 27.1 kbp | 23.6 kbp | 262.5 kbp | 1343 | 96.9% |
MaSuRCA | 339.2 Mbp | 30.6 kbp | 29.1 kbp | 219.4 kbp | 1288 | 96.7% | |
Platanus | 307.9 Mbp | 16.8 kbp | 16.6 kbp | 154.3 kbp | 367 | 95.6% | |
SOAPdenovo2 | 301.2 Mbp | 18.5 kbp | 18.3 kbp | 207.7 kbp | 91 | 97.1% | |
SparseAssembler | 155.3 Mbp | – | – | 43.0 kbp | 2 | 85.8% | |
S. pennellii | DISCOVAR | 851.9 Mbp | 66.4 kbp | 59.6 kbp | 1.3 Mbp | 4235 | 94.2% |
MaSuRCA | 884.2 Mbp | 61.3 kbp | 54.9 kbp | 617.2 Mbp | 6621 | 94.9% | |
Platanus | 641.3 Mbp | 15.4 kbp | 15.2 kbp | 270.1 kbp | 115 | 91.7% | |
SOAPdenovo2 | 768.5 Mbp | 28.2 kbp | 26.8 kbp | 323.3 kbp | 632 | 92.6% | |
SparseAssembler | 305.2 Mbp | – | – | 51.1 kbp | 11 | 76.5% | |
Z. mays | PhredPhrap+ABySS (GCA_000005005.5) | 2.0 Gbp | 40.0 kbp | 36.2 kbp | 849.5 kbp | 15,133 | 91.9% |
H. sapiens (CHM1) | SRPRISM+ARGO (GCF_000306695.2) | 2.8 Gbp | 127.5 kbp | 127.1 kbp | 1.0 Mbp | 106 | 80.3% |
H. sapiens (NA12878) | DISCOVAR (GCA_001517065.1) | 2.8 Gbp | 115.7 kbp | 115.3 kbp | 961.2 kbp | 336 | 83.7% |