Fig. 3

StrainGE is the only tool that can detect strain sharing at coverages as low as 0.5x. a Depiction of how synthetic Escherichia genomes were generated from randomly selected NCBI RefSeq genomes to create sets of closely related strains (e.g., A1/A2 and B1/B2) for spike in experiments. b Depiction of how spiked metagenomes were created using synthetic genomes from a. Each circle represents a spiked metagenome. The color of the circle indicates which synthetic strain was included: single color circles indicate spiked metagenomes containing a single synthetic strain, and two color circles indicate spiked metagenomes containing two synthetic strains mixed at equal proportions. c–e Precision-recall curves for each tool and coverage 0.1x–10x, when given the task to detect which sample pairs contain identical strains. The area under the curve (AUC) is depicted as a heatmap below. The “successful comparisons” bar plot indicates the percentage of sample pairs for which a comparison was possible (i.e., tools ran to completion for both samples). c Limiting to single-strain samples from distinct references. d Including samples with two strains, but limited to strains from distinct references. e Including samples with closely related strains