Table 1.
Assembly Results.
| Species | Sample (Total coverage, Read length N50) | Assembler | Sequence | Assembly Size (Mb) | # contigs (scaffods) | N50 size (Mb) | N50 # | N90 size (Mb) | Max Contig Size (Mb) |
|---|---|---|---|---|---|---|---|---|---|
| A. thaliana |
Inbred Col-0 (130x, read N50 = 9 kbp) |
Canu | contigs | 131 | 1102 | 4.573 | 8 | 0.0069 | 11.186 |
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| FALCON | p-contigs | 120 | 377 | 7.353 | 7 | 1.278 | 12.197 | ||
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|
Inbred Cvi-0 (120x, read N50 = 9 kbp) |
Canu | contigs | 127 | 676 | 4.817 | 9 | 0.364 | 12.393 | |
|
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| FALCON | p-contigs | 120 | 260 | 6.073 | 7 | 1.993 | 14.370 | ||
|
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|
F1 Col-0 x CVI-0 (120x, read N50 = 17 kbp) |
Canu | contigs | 219 | 1897 | 1.554 | 17 | 0.042 | 15.379 | |
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| FALCON | p-contigs | 143 | 426 | 7.923 | 6 | 0.387 | 13.386 | ||
| a-contigs | 57 | 551 | 0.146 | 117 | 0.05 | 0.688 | |||
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| FALCON-Unzip | p-contigs | 140 | 172 | 7.961 | 7 | 0.504 | 13.319 | ||
| haplotigs | 105 | 248 | 6.920 | 6 | 0.571 | 11.648 | |||
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|
F1 Col-0 x CVI-0 (short reads) (60x, 250 bp reads) |
Platanus | scaffolds | 143 | 151779 | 0.0269 | 1290 | 0.00014 | 0.329 | |
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| SOAPdenovo, k=93 | scaffolds | 260 | 691629 | 0.00099 | 43570 | 0.00013 | 0.0825 | ||
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| V. vinifera |
Cabernet Sauvignon (140x, read N50 = 15 kbp) |
Canu | contigs | 1066 | 14489 | 0.139 | 1778 | 0.03 | 2.211 |
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| FALCON | p-contigs | 633 | 1314 | 2.392 | 72 | 0.362 | 14.114 | ||
| a-contigs | 184 | 1164 | 0.278 | 220 | 0.073 | 0.804 | |||
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| Falcon Unzip | p-contigs | 591 | 718 | 2.173 | 72 | 0.402 | 14.079 | ||
| haplotigs | 368 | 2037 | 0.779 | 127 | 0.075 | 3.926 | |||
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|
Cabernet Sauvignon (short reads) (46x, 100 bp reads) |
SOAPdenovo, k=33 | scaffolds | 1728 | 12879081 | 0.0001 | 791053 | 0.0001 | 0.0368 | |
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| SOAPdenovo, k=43 | scaffolds | 507 | 767707 | 0.0019 | 63857 | 0.0018 | 0.0310 | ||
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| C. pyxidata |
Clavicorona pyxidata (100x, read N50=16 kb) |
Canu | contigs | 60 | 432 | 0.646 | 16 | 0.045 | 4.390 |
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| Falcon | p-contigs | 43 | 133 | 1.49 | 8 | 0.218 | 4.829 | ||
| a-contigs | 12 | 172 | 0.0805 | 41 | 0.037 | 0.407 | |||
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| Falcon Unzip | p-contigs | 42 | 82 | 1.484 | 8 | 0.252 | 4.778 | ||
| haplotigs | 24 | 93 | 0.872 | 9 | 0.141 | 2.218 | |||
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|
Clavicorona pyxidata (short reads) ( 86x, 100 bp reads) |
Platanus | scaffolds | 39 | 26702 | 0.045 | 225 | 0.0013 | 0.489 | |
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| SOAPdenovo, k=19 | scaffolds | 52 | 157941 | 0.00055 | 15065 | 0.00013 | 0.070 | ||