Fig. 4: Flow chart of the computational analysis.

Reads are mapped to the reference genomes by immap in two ways. For the analysis of rearrangements using paired-end reads, truncated (100 bp) reads mapped under stringent conditions are analyzed by midhr to identify rearrangements with unusual positions. Identified unusual pairs are subsequently clustered by sort_pdist and visualized by circmap. For the analysis of rearrangements using junction reads, reads (150 bp) mapped under mismatch-tolerant conditions are analyzed by midhr to identify and create junction clusters, and the clustered junction reads are visualized by circmap. The results of paired-end reads and junction reads are compared between strains by comp_mhmr.