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Table 2 Staphylococcus aureus USA300 assembly evaluation

From: De novo likelihood-based measures for comparing genome assemblies

  Contigs Scaffolds   
Assembler LAP LAP N50 (kb) CN50 (kb) LAP reads LAP mates N50 (kb) CN50 (kb) Unaligned Unaligned
  reads mates        reads mates
          (fraction) (fraction)
ABySS -16.608 -24.692 29.2 24.8 -16.611 -24.584 34 28 0.318 0.522
Allpaths-LG -18.018 -23.974 96.7 66.2 -18.018 -23.760 1,092 1,092 0.374 0.494
Bambus2 -18.083 -24.256 50.2 16.7 -18.085 -23.899 1,084 1,084 0.375 0.503
MSR-CA -18.282 -24.258 59.2 48.2 -18.282 -23.926 2,412 1,022 0.389 0.508
SGA -17.937 -27.019 4 4 -18.250 -24.906 208 208 0.384 0.578
SOAPdenovo -17.830 -23.892 288.2 62.7 -17.830 -23.862 332 288 0.362 0.499
Velvet -17.867 -24.258 48.4 41.5 -17.867 -23.925 762 126 0.363 0.503
S. aureus 04-02981 -19.960 -25.314 2,821 2,821 -19.960 -25.314 2,821 2,821 0.456 0.572
S. epidermidis -29.635 -29.951 2,499 2,499 -29.635 -29.951 2,499 2,499 0.972 0.988
truth -17.741 -23.509 2,873 2,873 -17.741 -23.509 2,873 2,873 0.358 0.473
  1. Assembly likelihood scores for Staphylococcus aureus USA300 from the GAGE project [15]. The results are presented separately for the contigs and scaffolds and include the number of unassembled reads (singletons), the LAP scores computed on unmated reads (LAP reads) or mate-pairs (LAP mates), the N50 contig/scaffold sizes (N50), and the reference-corrected N50 contig/scaffold sizes (CN50). The best (maximum) value for each genome-measure combination is highlighted in bold. The results for the reference assembly (either complete genome or high-quality draft) is given in the row marked truth. In addition, we provide the results for a closely related strain and species. All values, except the LAP scores, were taken from the GAGE publication. A threshold probability of 1e-30 was used for calculating the LAP scores. The standard deviations for the LAP’s reads and LAP’s mates scores are 0.00740 and 0.0105, respectively.