Fig. 3

Schematic diagram of chromosomal rearrangement analysis pipeline. Long DNA reads are aligned to a reference genome using LAST (blue box), then dnarrange finds rearranged reads and groups reads that overlap the same rearrangement (pink box). lamassemble merges/assembles each group of reads into a consensus sequence (yellow box). When there is a “complex” rearrangement (more than one group of rearranged reads is needed to understand the full structure of the rearrangement), dnarrange-link was used to infer the order and orientation of the groups and thereby reconstruct derivative chromosomes (green box)