Fig. 2

BayesPaths algorithm. This illustrates the BayesPaths algorithm for a single COG0532 from one MAG, Bin_55 of the ten sample synthetic data set. The algorithm predicted 3 strains. We show the input to the algorithm: A the unitig coverages across samples plus B the unitig graph without strain assignments. The outputs of the algorithm are shown in C the assignments of haplotypes to each unitig, D the strain intensities across samples, effectively coverage divided by read length (see “Methods - BayesPaths” section), and E unitig graphs for each haplotype with their most likely paths. This algorithm is explained in detail in the “Methods - BayesPaths” section