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Fig. 3 | Genome Biology

Fig. 3

From: DESMAN: a new tool for de novo extraction of strains from metagenomes

Fig. 3

Validation of reconstructed strains for the Escherichia coli O104:H4 outbreak. a The mean SNV uncertainty, i.e. the proportion of SNVs that a strain differs from its closest match in a replicate run, averaged over all the other replicates. This is shown on the y-axis against mean relative abundance across samples on the x-axis. b Phylogenetic tree constructed for the eight inferred strains found for the E. coli O104:H4 outbreak. The SCSGs for the strains and reference genomes were aligned separately using mafft [50], trimmed and then concatenated together. The tree was constructed using FastTree [51]. Inferred strains are shown as magenta, O104:H4 strains in red and uropathogenic E. coli in blue. Both results were for the run with G=8 that had the lowest posterior mean deviance. SNP single-nucleotide polymorphism, SNV single-nucleotide variant

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