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Table 3 Scaffolded assembly statistics after Hi-C analysis on HapSolo assemblies, for three primary assemblies for each of three species

From: HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding

Species Chardonnay Mosquito Thorny Skatef
Assembly type No HapSoloa HapSolo −HCb HapSolo +HCc No HapSolo HapSolo −HC HapSolo +HC No HapSolo HapSolo −HC HapSolo +HC
# of Scaffolds 1332 2748 2403 1211 603 611 14,238 12,269 10,009
% of Genome in k largest scaffoldsd,e 52.0% 89.0% 84.0% 61.9% 68.3% 85.7% 31.5% 104.7% 106.3%
% of Genome in Scaffolds > 10Mbe 44.0% 94.0% 94.0% 93.5% 94.7% 94.1% 40.4% 103.3% 105.5%
Scaffold assembly size (Mb) 656.1 570.4 540.1 212.5 200.8 200.3 3240 3158 3039
Largest scaffold (Mb) 19.1 32.6 36.5 43.6 53.0 95.0 170.0 208.4 250.5
Scaffold N50 (Mb) 7.2 23.5 20.7 37.9 41.5 41.6 62.1 65.5 69.8
Scaffold L50 28 11 11 3 3 2 16 35 13
  1. aResults in this column were based on the primary assembly without application of HapSolo
  2. bResults in this column were based on application of HapSolo without hill climbing (−HC) and default parameters of ID, Q and QR
  3. cResults in this column were based on application of HapSolo with 50,000 cycles of hill climbing (+HC)
  4. dPercentage of genome in the largest k scaffolds, where k is equal to the number of chromosomes expected for each species
  5. ePercentages normalized using expected genome sizes of 490 Mb, 200 Mb and 2560 Mb for chardonnay, mosquito and thorny skate respectively
  6. fResults for HapSolo were generated using minimap2