Fig. 3

Denoise joining-pairs by further considering end-assignments with orientation constraints. The top row of each case shows the combination of the end-labels and orientation of a joining-pair. The bottom row demonstrates the orientation of the two contigs with the joining-pair after scaffolding. Because of the way each read-pair is sequenced (i.e., facing each other), we must ensure that the two contigs are scaffolded in a way such that this expected orientation is not violated. There are four combinations (a–d of the end-assignments and the orientation satisfying these requirements. For example, 5′R + 3′F means that one end of the joining-pair is mapped to the 5′-most gene model in the reverse orientation, while the other end is mapped to the 3′-most gene model in the forward orientation. If we reverse both sequences, we can make a valid scaffold between the two contigs using the joining-pair