Figure 4

Statistics of assembly at each step of VirAmp. Cumulative data plots outputted by the QUAST package provide a visual overview of individual assembly steps, for a laboratory strain of HSV-1 (Table 2). Successive contigs are plotted in order from longest to shortest. In both graphs, the red line represents the output of the initial de novo assembly, the blue line represents the combination of multiple k-mer assemblies using reference-guided assembly approaches, and the green line represents the output after scaffolding by SSPACE. A) The first graph highlights the number of contigs (contig index, x-axis) needed to achieve the length of the trimmed reference genome (y-axis; 135 kb); this metric improves with successive steps of the VirAmp pipeline. Only contigs longer than 500 bp were considered to be valid. B) The second graph plots the percent of the genome (x-axis) covered as successive contigs are added, from longest to shortest. The y-axis intersect for each line is the length of the longest contig, and the line drops according to length of each successive contig. The black vertical line indicates NG50. The total length, largest contig, and NG50 all increase with each step of the VirAmp pipeline.