De novo likelihood-based measures for comparing genome assemblies

BMC Research Notes

Table 2 Staphylococcus aureus USA300 assembly evaluation

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.

ISSN: 1756-0500