Table 4.
A comparison of scaffolded assemblies after Hi-C analysis, based on HapSolo and purge_dups primary assemblies
| Speciesa | Chardonnay | Mosquito | Thorny Skate | |||
|---|---|---|---|---|---|---|
| Assembly type | HapSolo +HCb | purge_dups | HapSolo +HC | purge_dups | HapSolo +HCe | purge_dups |
| # of Scaffolds | 2403 | 294 | 611 | 635 | 10,009 | 1534 |
| % of Genome in k largest scaffoldsc | 88.0% | 58.5% | 85.7% | 83.7% | 106.3% | 86.8% |
| % of Genome in scaffolds > 10Md | 97.7% | 67.4% | 94.1% | 92.7% | 105.6% | 86.0% |
| Scaffold assembly size (Mb) | 540.1 | 470.4 | 200.4 | 200.3 | 3039.3 | 2251.4 |
| Largest scaffold (Mb) | 36.5 | 24.9 | 95.0 | 74.1 | 250.5 | 184.1 |
| Scaffold N50 (Mb) | 20.7 | 12.7 | 41.6 | 51.2 | 69.8 | 61.7 |
| Scaffold L50 | 11 | 15 | 2 | 2 | 13 | 11 |
aData for HapSolo are based on BLAT alignments for Chardonnay and mosquito, and minimap2 alignments for thorny skate
bResults in the +HC columns are based on application of HapSolo with 50,000 cycles of hill climbing (+HC)
cPercentage of genome in the largest k scaffolds, where k is equal to the number of chromosomes expected for each species. Percentages are normalized using expected genome sizes of 490 Mb, 200 Mb and 2560 Mb for Chardonnay, mosquito and thorny skate respectively
dPercentages normalized using expected genome sizes of 490 Mb, 200 Mb and 2560 Mb for chardonnay, mosquito and thorny skate respectively
eResults for HapSolo were generated using minimap2