File:Assessment-of-Metagenomic-Assembly-Using-Simulated-Next-Generation-Sequencing-Data-pone.0031386.g003.jpg

English: Scaffolds are constructed by linking contigs using information from paired end reads, during this process a number of unknown bases are usually found between the sequences of the linked contigs. To use the information obtained by scaffolding, Scaftigs can be constructed by extracting the contiguous sequences that lack unknown bases (Ns). a) Contig Length Distribution. Histograms of the contig lengths illustrate the number of contigs within a certain size fraction for assemblies of Illumina contigs (red) and Illumina scaftigs (light blue). Only contigs greater than 500 bp are shown, the x-axis is log scale. Assemblies were generated for different community complexities (10 genomes, 100 genomes, 400 genomes). b) Overall Accuracy of the Contigs. The overall accuracy of the contigs is summarized using different measures of chimericity. Bars to the left illustrate the percentage of all of the contigs that are chimeric, bars in the middle show the percentage of all of the contigs that have a Contig Score less than 95%, and to the right contigs that have a Contig Score less than 99%. Contig Score represents the percent identity between the contig and the derived reference genome. Illumina contigs are in red Illumina scaftigs are blue. c) Contig Accuracy across Contig Lengths. These combined strip plots show the degree of chimericity (upper plot) and contig score (lower plot) for each contig in the assemblies, each dot represents one contig. They are grouped into size bins. The degree of chimericity is the proportion of reads in a contig that are derived from the ‘wrong’ genome and thus make the contig chimeric. Contig Score represents the percent identity between the contig and the derived reference genome. Again Illumina contigs are in red and Illumina scaftigs are in blue.