English: a) Correlations between expected and actual COG abundance. Dotplots compare the expected and actual abundance for each COG, with the x-axis displaying the COG abundances as expected from the input genomes and the y-axis displaying the COG abundances as determined from assembly and annotation of the simulated metagenomes. The black line shows the 1∶1 correlation. The Pearson correlation coefficients are displayed for each dataset. b) Principal Coordinate Analysis (PCoA) and Principal Component Analysis (PCA). The COG abundance profiles were compared to each other using Jensen-Shannon divergence and the distance matrix was then analyzed plotted using PCoA. The COG abundance profiles were analyzed plotted using PCA. The dots are colored by sequencing method: Illumina contigs (red), Illumina scaftigs (light blue), Sanger (yellow) and pyrosequencing (blue).