@rfolkert If PE reads don't merge then we concatenate them with a short internal spacer, so we do treat them as "linked". When using a reference it's handled exactly the same way. R1 and R2 are mapped jointly. We test to make sure the mapping is "sane" (on the same chromosome, the orientation is right, etc, etc,) then we merge them. If they do not merge we concatenate them with a spacer and continue the assembly.