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Table 3 Homo sapiens chr 14 assembly evaluation

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

  Contigs Scaffolds    
Assembler LAP LAP N50 (kb) CN50 (kb) LAP LAP N50 (kb) CN50 (kb) CGAL Score Unaligned Unaligned
  reads mates    reads mates     reads mates
           (fraction) (fraction)
ABySS -18.473 -23.801 2 2 -18.474 -23.787 2.1 2 -15.21×108 0.257 0.504
Allpaths-LG -15.813 -21.413 36.5 21 -15.824 -21.314 81,647 4,702 -13.11×108 0.115 0.239
Bambus2 -18.606 -23.474 5.9 4.3 -18.642 -23.343 324 161 - 0.258 0.422
CABOG -15.625 -21.128 45.3 23.7 -15.626 -21.041 393 26 -12.25 × 1 08 0.109 0.229
MSR-CA -16.421 -22.428 4.9 4.3 -16.436 -21.861 893 94 - 0.122 0.276
SGA -15.712 -22.990 2.7 2.7 -16.909 -22.326 83 79 - 0.134 0.328
SOAPdenovo -15.702 -21.705 14.7 7.4 -15.734 -21.594 455 214 * 0.101 0.269
Velvet -18.000 -23.468 2.3 2.1 -18.140 -23.375 1,190 27 - 0.214 0.442
truth -15.466 -21.001 107,349.50 107,349.50 -15.466 -21.002 107,349.50 107,349.50 -11.25 ×108 0.093 0.211
  1. Assembly likelihood scores for human chromosome 14 from the GAGE project [15] using a 10,000 read sample. 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. CGAL scores calculated from the long insert library were taken from the CGAL publication. The authors only provided scores for the top three assemblies (Bowtie2 could not successfully map reads to the SOAPdenovo assembly). All values, except the LAP and CGAL scores, were taken from the GAGE publication. A threshold probability of 1e-30 was used for calculating the LAP scores. The standard deviation for both the LAP’s reads and LAP’s mates scores is 0.15.