Fig. 4

a Relative abundance predictions across the synthetic sample sets, using randomly selected strains from the d50 and d100 database for QuantTB only. If the strain was correctly predicted for the sample it is colored green (true positive), whereas incorrectly predicted strains are colored red (false positive). The left graph contains samples where two strains are present at 1× and 9× coverage. The right graph contains samples where two strains are present at 3× and 7× coverage. b Predicted relative abundances across synthetically mixed samples for QuantTB, StrainSeeker and Sigma. Each point represents a predicted relative abundance for a single strain. Each mixed sample contained a pair of strains from the d50 dataset at either 1 × − 9× or 3 × − 7× abundance. Although samples were sourced from the d50 dataset, the tools used a different set of genomes as a reference set (sourced from d10). Thus genomes in the samples were not present in the underlying database the tools were trained on. This lets us see how well each tool is at predicting the correct number of strains and the correct relative abundance between strains if the ‘correct’ strain in the sample is not already present in the database