Fig. 3.

Fragment generation by stitching and overhang trimming of readpair (r₁, r₂). (a) r₁ and r₂ are represented as arrows facing each other denoting the forward and reverse complement strands. The green bars denote one of the shared kmers between them, which is an anchor for suffix—prefix alignment. The stitched fragment is a concatenation of prefix of r₁, overlap and suffix of r₂. (b) When r₁ and/or r₂ extends beyond the $5\prime$ region of the other read, the overhang is trimmed, and f is the overlap. (c) When r₁ and r₂ cannot be merged, f is a concatenation of r₁ and reverse complement of r₂