Figure 5

A chain of seeds guides a local transition alignment across multiple genomic loci. High-quality seeds mapping to different genomic loci, strands or chromosomes (A) are chained. Subsequently, the order of the seeds within the chain guides a walk through the alignment cube (B). For each genomic locus, a local alignment with the read is performed. In addition to the regular Smith-Waterman recursions, the local transition alignment allows crossing between different reference loci.