Mate-pair signatures for rearrangement style mis-assemblies. (a) Three copy repeat R, with interspersed unique sequences B and C, shown with properly sized and oriented mates. (b) Mis-assembled repeat shown with mis-oriented and expanded mate-pairs. The mis-assembly is caused by co-assembled reads from different repeat copies, illustrated by the stacked repeat blocks.
Phillippy et al. Genome Biology 2008 9:R55 doi:10.1186/gb-2008-9-3-r55