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 |