Table 4 The performances of tested scaffolders for A. thaliana, S. pennellii, and H. sapiens using Nanopore long reads
From: LRScaf: improving draft genomes using long noisy reads
Species | Method | Sum | NG50 | NGA50 | Longest | Mis. (#) | BUSCO (Complete) | CPU Time (Hours) | Peak Memory (GB) |
|---|---|---|---|---|---|---|---|---|---|
A. thaliana (KBS-Mac-74) | DBG2OLC (SA) | 150.4 Mbp | 2.6 Mbp | – | 12.2 Mbp | – | 25.9% | 2.9 | 18.9 |
MaSuRCA-Hy (MSR) | 123.2 Mbp | 2.5 Mb | 2.3 Mbp | 9.2 Mbp | 211 | 98.3% | 145.6 (17.9) | 60.3 | |
OPERA-LG (SA) | 116.4 Mbp | 7.3 Mbp | 2.8 Mbp | 14.3 Mbp | 102 | 97.2% | 188.9 | 45.9 | |
SMIS (SOAP) | 116.2 Mbp | 10.3 Mbp | 2.4 Mbp | 15.0 Mbp | 180 | 98.2% | 2391.7 | 26.8 | |
SSPACE-LR (PLA) | 120.6 Mbp | 3.2 Mbp | 2.2 Mbp | 6.8 Mbp | 178 | 98.4% | 104.6 | 9.0 | |
LRScaf (DIS) | 123.1 Mbp | 9.0 Mbp | 4.9 Mbp | 12.4 Mbp | 115 | 98.3% | 0.5 | 21.4 | |
S. pennellii | DBG2OLC (SA) | 1.5 Gbp | 243.7 kbp | – | 1.7 Mbp | – | 18.9% | 27.0 | 21.6 |
MaSuRCA-Hy (MSR) | 950.4 Mbp | 331.1 kbp | 159.6 kbp | 3.1 Mbp | 17,957 | 95.6% | 1389.1 (202.8) | 239.7 | |
OPERA-LG (DIS) | 952.0 Mbp | 730.0 kbp | 280.1 kbp | 3.5 Mbp | 11,404 | 92.1% | 286.6 | 25.4 | |
SSPACE-LR (DIS) | 871.1 Mbp | 82.9 kbp | 69.5 kbp | 1.3 Mbp | 6796 | 94.7% | 650.0 | 13.1 | |
LRScaf (DIS) | 952.8 Mbp | 794.4 kbp | 441.3 kbp | 5.4 Mbp | 5150 | 95.8% | 3.1 | 36.8 | |
H. sapiens (NA12878) | LRScaf | 2.9 Gbp | 17.4 Mbp | 12.9 Mbp | 64.2 Mbp | 785 | 94.9% | 2.1 | 62.6 |