Fig. 4

Estimation of diversity metrics of tool-predicted virome populations. To assess the impact of each tool on population diversity, four simulated virome assemblies from Roux et al. [57] were downloaded. Each programme was then run to determine the subset of predicted viral contigs. Reads were mapped to these contig subsets, and mapped reads were then subsequently mapped to a pool of population contigs. All diversity metrics were computed by the R package “vegan”. “Default” in each plot indicates each sample’s original assembly. A Number of genomes observed from read mapping to predicted viral contig populations for each tool. B Comparison of estimated Shannon diversity indices from each tool’s virome subset. Estimations are based on read counts that were normalised by contig size and sequencing depth of the virome. C Comparison of Simpson diversity indices from each tool’s virome subset. D Nonmetric multidimensional scaling (NMDS) ordination plot of Bray-Curtis dissimilarity of virome subsets predicted by each viral identification tool. Ellipses indicate the 95% confidence interval for each sample cluster’s centroid. Samples are represented by the same symbol and ellipse line type; tools are denoted by colour