TABLE 1.
Feature | Canu 1.8 contigs | Canu 1.8 contigs + Purge Haplotigs | Canu 1.8 unitigs | Flye 2.6 | MaSuRCa-CA 3.3.9 | MaSuRCa-Flye 3.3.9 | Shasta 0.4.0 | wtdbg2 2.5 |
Number of contigs (all contigs) | 101 | 35 | 192 | 90 | 87 | 388 | 1069 | 348 |
Number of contigs (length > 5 kb) | 101 | 35 | 192 | 77 | 87 | 140 | 389 | 345 |
Number of contigs (length > 50 kb) | 75 | 32 | 111 | 55 | 78 | 104 | 137 | 109 |
Largest contig, Mb | 6.75 | 6.76 | 6.75 | 6.69 | 4.56 | 4.33 | 5.78 | 5.94 |
Total length, Mb (all contigs) | 70.9 | 59.2 | 73.8 | 69.1 | 69.2 | 68.4 | 66.2 | 65.0 |
Total length, Mb (contigs > 5 kb) | 70.9 | 59.2 | 73.8 | 69.1 | 69.2 | 67.8 | 65.0 | 65.0 |
Total length, Mb (contigs > 50 kb) | 70.0 | 59.1 | 71.0 | 68.7 | 68.9 | 67.3 | 61.6 | 60.8 |
N50, Mb | 3.13 | 3.35 | 2.19 | 3.77 | 2.07 | 1.61 | 2.19 | 2.93 |
N75, Mb | 1.25 | 2.19 | 0.72 | 1.19 | 0.94 | 0.50 | 0.29 | 0.37 |
L50 | 8 | 7 | 9 | 7 | 11 | 13 | 10 | 9 |
L75 | 17 | 12 | 24 | 16 | 23 | 32 | 35 | 24 |
GC, % | 47.95 | 47.98 | 47.91 | 47.99 | 48.13 | 48.08 | 48.03 | 47.99 |
Canu contigs + Purge Haplotigs, contigs derived with Canu and then filtered with Purge Haplotigs; MaSuRCa-CA, MaSuRCa pipeline coupled with Celera Assembler; MaSuRCa-Flye, MaSuRCa pipeline coupled with Flye.