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Table 1 Rhodobacter sphaeroides 2.4.1 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 -20.924 -27.365 5.9 4.2 -20.929 -27.320 9 5 0.228 0.524
Allpaths-LG -20.795 -27.141 42.5 34.4 -20.796 -27.099 3,192 3,192 0.212 0.441
Bambus2 -21.528 -27.439 93.2 12.8 -21.531 -27.424 2,439 2,419 0.270 0.501
CABOG -22.550 -27.749 20.2 17.9 -22.550 -27.714 66 55 0.345 0.540
MSR-CA -21.496 -27.407 22.1 19.1 -21.497 -27.324 2,976 2,966 0.268 0.478
SGA -20.896 -27.575 4.5 2.9 -21.030 -27.416 51 51 0.237 0.541
SOAPdenovo -20.816 -27.160 131.7 14.3 -20.816 -27.152 660 660 0.214 0.453
Velvet -20.903 -27.314 15.7 14.5 -20.907 -27.246 353 270 0.219 0.471
R. sphaeroides ATCC 17025 -29.391 -29.973 3,218 3,218 -29.391 -29.973 3,218 3,218 0.813 0.904
R. capsulatus -29.953 -29.997 3,739 3,739 -29.953 -29.997 3,739 3,739 0.978 0.995
truth -20.769 -27.071 3,189 3,189 -20.769 -27.071 3,189 3,189 0.209 0.432
  1. Assembly likelihood scores for Rhodobacter sphaeroides 2.4.1 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 0.00685 and 0.00969, respectively.