Fig. 5.

There are six contigs (c₁,c₂,c₃,c₄,c₅,andc₆) that can be aligned with the long read lr₁. Because c₁ and c₂ are simultaneously aligned with the left end of lr₁, SLR retains only contig c₁ which has the greatest alignment length, and deletes the alignment information between c₂ and lr₁. Because c₅ and c₆ have been simultaneously aligned with the right end of lr₁, we keep only c₅, and delete the alignment information between c₆ and lr₁. Finally, SLR determines the orders and orientations of c₁, c₃, c₄ and c₅, which form a local scaffold