Table 4 The effect of the map density on the assembly of the C. elegans data
Method | # of markers | # of contigs | NGA50 (bp) | Genome fraction | Misassemblies | BUSCO Compl. (%) | Reads mapped (%) | Runtime (min) | Peak memory (MB) |
|---|---|---|---|---|---|---|---|---|---|
Kermit | 1k | 850 | 89,141 | 74.315 | 13 | 73.4 | 91.84 | 21 | 11,943 |
Kermit | 10k | 733 | 82,640 | 68.808 | 16 | 67.8 | 90.69 | 21 | 11,809 |
Kermit | 20k | 216 | 818,928 | 95.417 | 9 | 93.8 | 98.09 | 22 | 12,434 |
Kermit | 50k | 69 | 3,450,849 | 99.539 | 12 | 98.0 | 99.74 | 23 | 12,542 |
Kermit | 100k | 61 | 3,476,344 | 99.563 | 11 | 98.3 | 99.75 | 23 | 12,543 |
Kermit | 150k | 64 | 3,450,700 | 99.555 | 12 | 98.1 | 99.77 | 23 | 12,555 |
Kermit | 200k | 64 | 3,476,344 | 99.563 | 11 | 98.3 | 99.75 | 23 | 12,542 |
Kermit | 500k | 64 | 3,476,344 | 99.563 | 11 | 98.2 | 99.75 | 23 | 12,544 |
HGGA | 1k | 69 | 2,488,265 | 95.627 | 8 | 93.8 | 97.63 | 38 | 1902 |
HGGA | 10k | 44 | 3,668,792 | 99.698 | 9 | 97.9 | 99.75 | 40 | 1837 |
HGGA | 20k | 44 | 3,668,641 | 99.680 | 10 | 95.6 | 98.52 | 42 | 1835 |
HGGA | 50k | 46 | 3,668,702 | 99.708 | 9 | 95.9 | 98.52 | 42 | 1827 |
HGGA | 100k | 49 | 3,668,667 | 99.646 | 9 | 97.8 | 99.78 | 42 | 1874 |
HGGA | 150k | 51 | 3,668,731 | 99.669 | 8 | 98.1 | 99.75 | 42 | 1886 |
HGGA | 200k | 52 | 3,869,053 | 99.568 | 8 | 96.2 | 99.36 | 43 | 1833 |
HGGA | 500k | 47 | 3,668,735 | 99.652 | 13 | 98.0 | 99.76 | 48 | 1837 |