Table 2 Qualitative comparison of the output scaffolds generated by the different tools on the different inputs. All statistics shown are for the final output scaffolds, and were calculated using the Quast tool. Symbol − indicates that the corresponding runs did not complete within 6 h; and \(*\) indicates that no NGA50 were obtained from the Quast results. Bold face values show the best results for any input
From: Maptcha: an efficient parallel workflow for hybrid genome scaffolding
Input | Method | NG50 | NGA50 | Largest Alignment (bp) | Genome Coverage % | Missassemblies | Duplication Ratio |
|---|---|---|---|---|---|---|---|
E. coli | LRScaf | 4,499,158 | 3,541,973 | 3,541,973 | 97.12 | 0 | 1.03 |
ntLink | 4,653,131 | 4,495,406 | 4,495,406 | 96.96 | 1 | 1.04 | |
Maptcha | 4,641,652 | 4,641,652 | 4,641,652 | 99.87 | 0 | 1 | |
P. aeruginosa | LRScaf | 3,780,771 | 3,703,369 | 3,703,369 | 97.96 | 1 | 1.03 |
ntLink | 4,734,796 | 3,640,841 | 3,640,841 | 97.21 | 1 | 1.03 | |
Maptcha | 6,264,404 | 6,264,404 | 6,102,781 | 98.69 | 0 | 1 | |
C. elegans | LRScaf | 1,080,091 | 1,080,091 | 5,019,647 | 83.68 | 46 | 1.23 |
ntLink | 818,712 | 435,226 | 3,007,944 | 77.34 | 35 | 1.25 | |
Maptcha | 15,736,218 | 15,736,218 | 17,718,942 | 99.81 | 11 | 1 | |
T. crassiceps | LRScaf | 171,559 | 128,433 | 1,108,210 | 86.86 | 501 | 1.02 |
ntLink | 564,569 | 478,734 | 3,925,088 | 84.26 | 20 | 1.05 | |
Maptcha | 4,805,993 | 2,716,011 | 12,352,928 | 98.68 | 21 | 1 | |
D. busckii | LRScaf | 2,597,298 | 1,129,460 | 13,199,135 | 91.41 | 42 | 1.11 |
ntLink | 1,598,290 | 335,476 | 10,477,172 | 84.75 | 17 | 1.13 | |
Maptcha | 13,533,287 | 13,432,400 | 23,381,820 | 95.69 | 0 | 1.01 | |
Human chr 7 | LRScaf | 4,499,158 | 4,499,158 | 3,541,973 | 97.12 | 0 | 1.03 |
ntLink | 872,912 | 245,860 | 4,336,964 | 60.69 | 33 | 1.44 | |
Maptcha | 81,166,983 | 81,144,021 | 81,144,021 | 99.71 | 2 | 1 | |
N. polychloros | LRScaf | – | – | – | – | − | |
ntLink | 449,932 | 66,222 | 2,556,669 | 55.50 | 273 | 1.61 | |
Maptcha | 13,933,406 | 13,338,748 | 18,337,428 | 99.92 | 15 | 1 | |
C. septempunctata | LRScaf | − | – | – | – | – | |
ntLink | 81,127 | \(*\) | 2,243,121 | 34.31 | 236 | 1.83 | |
Maptcha | 24,570,419 | 21,121,362 | 40,568,023 | 99.95 | 25 | 1 | |
B. splendens | LRScaf | − | − | − | – | – | |
ntLink | 890,090 | 548,569 | 6,269,807 | 73.08 | 190 | 1.15 | |
Maptcha | 18,757,076 | 16,788,131 | 31,409,892 | 99.01 | 54 | 1.1 | |
M. florea | LRScaf | − | – | – | − | – | |
ntLink | 453,387 | \(*\) | 2,806,031 | 45.03 | 266 | 1.74 | |
Maptcha | 34,041,601 | 15,241,540 | 24,515,726 | 97.91 | 67 | 1 | |
H. aestivaria | LRScaf | − | – | − | − | – | |
ntLink | 37,703 | \(*\) | 901,904 | 30.73 | 441 | 2.08 | |
Maptcha | 18,646,319 | 9,640,658 | 29,935,333 | 99.83 | 34 | 1 |