Table 3. De novo assembly statistics.
| L. virgatum Illumina | L. vulgare Illumina | L. vulgare hybrid assembly | L. vulgare Nanopore | |
|---|---|---|---|---|
| input reads (post-trimming in Canu) | 212,186 | 248,456 | 14,351 (10,422) | 8,338 (4,632) |
| best k-mer | 65 | 55 | n.a. | n.a. |
| no. of Leucanthemum contigs (after splitting) | 5 | 3 | 5 (7) | 5 (6) |
| contig sizes | 621–82,641 bp | 18,400–82,675 bp | 6,819–54,677 bp | 6,655–53,891 bp |
| mean coverage (stdev) | 128.30x (109.88) | 152.28x (113.00) | 559.39x (323.29) | 321.43x (167.74) |
| fraction at coverage x or higher | 30x: 93.38% 20x: 98.66% | 30x: 99.74% 20x: 99.91% | 100x: 99.71% 50x: 99.77% | 100x: 91.17% 50x: 99.83% |
Three de novo assemblies were produced for L. vulgare, using Illumina data, Nanopore data or Nanopore data improved by Illumina data (hybrid approach using Nanocorr). Assembly was done with Unicycler for Illumina reads and Canu for Nanopore reads. Nanopore input reads are also given after Canu correction and trimming steps (in brackets). Number of contigs is given before and after splitting by Exonerate for further use. Values for "fraction at coverage x or higher" refer to the final assembled sequence without the IRA and denote the percentage with a certain read coverage after mapping of input reads.
L., Leucanthemum; stdev, standard deviation; no, number; n.a., not applicable.