Schematic map of scaffolding. A. Red arrows represent repeat contigs, and black and blue arrows represent unique contigs, where the orientation of the arrow represents the direction from the 5’ to 3’ end. The purple lines represent mate-pair reads within contigs whereas green and yellow lines represent mate-pair reads spanning contigs. The mate-pair reads represented by yellow lines are mapped into unique contigs and thus they can form a scaffold. Mate-pair reads represented by green lines failed to construct scaffolds because one end of these mate-pair reads is located in repeat contigs. B. Using ContigScape to describe graph A.
Tang et al. BMC Genomics 2013 14:289 doi:10.1186/1471-2164-14-289