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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
  1. aLINKS-Nanocorr are derived from re-scaffolding baseline Illumina assemblies with Nanocorr-corrected ONT reads whereas CA-Nanocorr (polished)-LINKS is derived from re-scaffolding the CA-Nanocorr (polished) assembly [8, 17] with raw ONT W303 reads
  2. bBest genome assembly metrics are highlighted in Bold