Fig. 4

A de novo genome assembly of Porphyromonas gingivalis artificial reads. a. Eleven programs were used for de novo assembly of the seven strains in study. The main cumulative lengths were calculated, and plotted here against the contig index. b. The three assemblers that produced the highest N50 were plotted in the same manner as in a. (upper panel), then the assembly was mapped to the reference and only the mapped contigs were plotted (lower panel). c. The number of contigs (A5-miseq and SPAdes) was plotted against the amount of repeats (with at least 3 copies). d. Identification of gaps: after assembly with A5-miseq or SPAdes, genomic regions not covered by contigs were extracted. The gaps were classified into five categories: genomic islands, ribosomal RNA (rrn) operons, coding sequences (CDS) with repeated domains, intergenic sequences, and insertion sequences or miniature inverted-repeat transposable element (IS/MITEs)