Table 2 QUAST analysis of baseline and re-scaffolded E. coli K-12, S. Typhi H58, S. cerevisiae S288c and W303 assemblies using Oxford Nanopore Technologies reads
From: LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads
Genome | Method | Data/Chemistry/ Fold coverage | Number of contigs (> = 500 bp) | NG50 length (bp) | NA50 length (bp) | Number of genes | Number of N’s per 100 kbp | Number of mis-assemblies | Mis-assemblies type relocations/Trans-locations/Inversions |
|---|---|---|---|---|---|---|---|---|---|
E. coli K-12 | Baseline | Illumina | 61 | 206,356 | 177,531 | 4,443 | 113.61 | 5 | 5/0/0 |
AHA | F2D/R7/4.7x | 46 | 226,696 | 179,569 | 4,441 | 390.31 | 12 | 12/0/0 | |
2D/R7/34.2x | 34 | 480,126 | 266,663 | 4,441 | 719.89 | 21 | 21/0/0 | ||
Raw/R7.3/67.0x | 30 | 762,313 | 344,280 | 4,443 | 523.61 | 9 | 9/0/0 | ||
LINKS | F2D/R7/4.7x | 27 | 633,147 | 293,772 | 4,443 | 325.95 | 11 | 11/0/0 | |
2D/R7/34.2x | 16 | 1,197,321 | 294,667 | 4,440 | 566.97 | 20 | 20/0/0 | ||
Raw/R7.3/67.0x | 27 | 645,797 | 344,280 | 4,443 | 401.61 | 9 | 9/0/0 | ||
CA-Nanocorr | Raw/R7/145x | 1 | 4,654,420 | 2,768,544 | 4,515 | 0.00 | 5 | 4/0/1 | |
CA-Nanopolish | 2D/R7.3/29x | 1 | 4,593,653 | 2,739,950 | 4,515 | 0.00 | 2 | 2/0/0 | |
CA-NaS | 2D/R7/30x | 1 | 4,654,321 | 3,507,873 | 4,515 | 0.00 | 2 | 2/0/0 | |
SSPACE-LR | F2D/R7/4.7x | 43 | 226,696 | 215,056 | 4,448 | 388.10 | 8 | 8/0/0 | |
2D/R7/34.2x | 37 | 300,940 | 216,050 | 4,446 | 682.61 | 11 | 11/0/0 | ||
Raw/R7.3/67.0x | 39 | 238,960 | 226,324 | 4,448 | 539.84 | 8 | 8/0/0 | ||
S. Typhi H58 | Baseline | Illumina | 86 | 153,674 | 114,216 | 4,305 | 0.00 | 9 | 8/0/1 |
AHA | 2D/R7/4.7x | 38 | 472,758 | 267,543 | 4,308 | 213.33 | 22 | 20/0/2 | |
LINKS | 22 | 652,465 | 332,188 | 4,313 | 434.83 | 21 | 20/0/1 | ||
SPAdes | 34 | 319,375 | 282,035 | 4,344 | 0.00 | 14 | 12/0/2 | ||
SSPACE-LR | 29 | 473,660 | 280,966 | 4,331 | 236.65 | 21 | 20/0/1 | ||
S. cerevisiae S288c | Baseline | Illumina | 1,673 | 10,038 | 10,671 | 5,117 | 86.66 | 18 | 8/10/0 |
AHA | Raw/R7/119.9x | 363 | 141,253 | 78,176 | 5,325 | 4,996.13 | 173 | 127/46/0 | |
LINKS | 189 | 288,075 | 173,906 | 5,269 | 3,989.86 | 66 | 23/43/0 | ||
LINKS-Nanocorra | Nanocorr/40.3x | 224 | 645,967 | 150,299 | 5,282 | 15,469.63 | 160 | 72/88/0 | |
SSPACE-LR | Raw/R7/119.9x | 472 | 220,727 | 129,088 | 5,363 | 10,646.35 | 140 | 32/106/2 | |
S. cerevisiae W303 | Baseline | Illumina | 4,021 | 59,927 | 49,258 | 6,018 | 3,989.86 | 76 | 20/56/0 |
AHA | Raw/R7/119.9x | 3,706 | 440,962 | 168,384 | 6,040 | 1603.59 | 149 | 43/106/0 | |
LINKS | 3,782 | 334,705 | 176,649 | 6,030 | 784.78 | 97 | 27/72/0 | ||
LINKS-Nanocorra | Nanocorr/40.3x | 3,671 | 640,472 | 165,312 | 6,035 | 2,171.54 | 161 | 41/120/0 | |
CA-Nanocorr | 95 | 585,890 | 263,428 | 6,247 | 0.00 | 166 | 76/90/0 | ||
CA-Nanocorr (polished) | 95 | 585,932 | 263,474 | 6,250 | 0.00 | 168 | 77/90/1 | ||
CA-Nanocorr (polished)-LINKSa | Raw/R7/119.9x | 93 | 585,932 | 263,474 | 6,250 | 24.05 | 169 | 80/88/1 | |
CA-NaS | 13x of >10 kb reads | 121 | 159,881 | 109,441 | 6,016 | 0.00 | 146 | 76/70/0 | |
SSPACE-LR | Raw/R7/119.9x | 3,249 | 354,977 | 126,601 | 6,044 | 10,953.41 | 173 | 41/132/0 |