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Table 1 QUAST analysis of a baseline E. coli assembly and re-scaffolded assemblies using Oxford Nanopore 2D (R7 chem.) or raw (R7.3 chem.) reads

From: LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads

Stats based on sequences ≥ 500 bp A. ABySS contigs B. ABySS scaffolds C. LINKS k15d4000 D. LINKS k15d4000 E. SSPACE-LR g200 F. LINKS x30 k15d500–16kbp G. LINKS x30 k15d500–16kbp H. LINKS x30 k15d500–16kbp
Input data Illumina MiSeq A. +MiSeq A. +ONT Full 2D R7 B. + ONT Full 2D R7 B. +ONT Full 2D R7 B. +ONT Full 2D R7 B. +ONT All 2D R7 B. +raw ONT R7.3
Read input fold coverage 241.2x 241.2x 4.7x 4.7x 4.7x 4.7x 34.2x 67.0x
Time (h:mm:ss) - - 0:01:35 0:01:32 0:01:09 0:17:43 1:50:25 3:04:11
Memory (GB) - - 2.1 2.1 0.7 4.3 27.2 46.7
Total sequences 67 61 49 48 43 27 16 26
Largest (bp) 358,719 406,793 633,204 633,147 628,411 1,057,556 1,286,148 1,286,419
NG50 length (bp) 179,720 206,356 270,992 293,925 226,696 633,147 1,197,321 645,796
Misassemblies 5 5 5 5 8 11 20 9
Genes + parts 4,442 + 63 4,443 + 62 4,443 + 62 4,443 + 62 4,448 + 57 4,443 + 62 4,440 + 62 4,443 + 62
Max.alignment (bp) 358,223 405,659 486,572 486,527 405,659 760,934 760,934 759,131
Number of N’s per 100 kbp 109.74 113.61 189.32 192.88 388.10 325.95 566.97 401.61
NGA50 (bp) 177,531 179,569 228,879 228,879 226,324 299,206 299,206 486,527
NA50 (bp) 146,850 177,531 226,324 226,324 215,056 293,772 294,667 344,280