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Table 2 Gap closure results obtained on the eukaryotic datasets

From: Toward almost closed genomes with GapFiller

  Method
  Original SOAPdenovo GapFiller
Saccharomyces cerevisiae    
   Genome size (bp) 11,388,647 11,388,600 11,388,609
   Scaffolds 334 334 334
   Gap count 283 67 45
   Total gap length (bp) 19,358 994 2,873
   Errors (SNPs) 890 1,033 931
   Errors (indels) 565 754 648
   Errors (misjoins) 23 42 31
   N50 84,640 84,640 84,649
Homo sapiens (chromosome 14)    
   Genome size (bp) 95,081,274 95,059,687 95,072,801
   Scaffolds 19,249 19,249 19,249
   Gap count 2,820 1,986 1,682
   Total gap length (bp) 949,137 423,107 699,550
   Errors (SNPs) 76,653 79,266 76,928
   Errors (indels) 21,261 23,144 22,338
   Errors (misjoins) 179 224 187
   N50 7,748 8,262 8,469
  1. Results of SOAPdenovo and GapFiller obtained for the S. cerevisiae and human genome show the suitability of both methods to close gaps also in eukaryotic genomes. Patterns are similar to the observations made for bacteria: overall, GapFiller yields the most reliable results and the lowest gap count whereas SOAPdenovo yields a significantly shorter total gap length (though at the cost of a fairly increased error rate). In human the shortened genome size and total gap length obtained by SOAPdenovo (together with the increased indel and misjoin error rate) might indicate that some gaps are eventually closed by collapsing of (repeated) elements.