Table 1.
A comparison of genome assembly results for myrtle rust using different de novo assemblers.
| De novo assembler | Total # of contigs | N503 (bp) | Max Contig (bp) | Total length (bp) | |
|---|---|---|---|---|---|
| Readjoiner (ol = 70) | all | 4,963,090 | 439 | 3099 | 2,147,976,637 |
| 2l ≥ 750 | 116,914 | 859 | 103,828,908 | ||
| SGA (1ol = 85) | all | 1,321,742 | 493 | 8631 | 573,387,137 |
| l ≥ 750 | 135,453 | 976 | 137,671,501 | ||
| AbySS (k = 45) | all | 759,095 | 558 | 25,668 | 362,000,000 |
| l ≥ 750 | 99,806 | 1522 | 145,365,606 | ||
| SOAPdenovo (k = 127) | all | 766,280 | 567 | 6094 | 387,909,377 |
| l ≥ 750 | 109,692 | 949 | 108,060,557 | ||
| CLC-Bio (k = 40) | all | 148,139 | 3165 | 47,187 | 387,958,276 |
| l ≥ 750 | 148,138 | 3165 | 387,956,878 | ||
| l ≥ 3000 | 37,684 | 5535 | 203,507,520 | ||
| l ≥ 4000 | 23,106 | 7929 | 153,506,636 |
Notes: 1overlap length;
2
contig length (bp);
3
An N50 contig size of N means that 50% of the assembled bases are contained in contigs of length N or larger. N50 sizes are often used as a measure of assembly quality because they capture how much of the genome is covered by relatively large contigs.