Fig. 7

Constructing edges from alignment. a Read positions and orientations generated from the target genome. b If the reference genome does not have rearrangements, the read should be concordantly aligned to the reference genome. An edge is added to connect the right end of u to the left end of v. Traversing the two segments along the edge reads out u·v, which is the same as the reference. c Both ends of the read align to the forward strand. An edge is added to connect the right end of u to the right end of rev(v). Traversing the segments along the edge reads out sequence u· rev(rev(v))=u·v, which recovers the target sequence and the read can be concordantly aligned. d If both ends align to the reverse strand, an edge is added to connect the left end of the front segment to the left end of the back segment. e If two ends of a read point away from each other, an edge is added to connect the left end of the front segment to the right end of the back segment