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Table 4 A comparison of scaffolded assemblies after Hi-C analysis, based on HapSolo and purge_dups primary assemblies

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

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
  1. aData for HapSolo are based on BLAT alignments for Chardonnay and mosquito, and minimap2 alignments for thorny skate
  2. bResults in the +HC columns are based on application of HapSolo with 50,000 cycles of hill climbing (+HC)
  3. 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
  4. dPercentages normalized using expected genome sizes of 490 Mb, 200 Mb and 2560 Mb for chardonnay, mosquito and thorny skate respectively
  5. eResults for HapSolo were generated using minimap2