@SpPapakostas_twitter The datatype should be consistent with your library prep protocol. Did you do the library prep or did you have it done by the sequencing facility? If you have paired end original RAD protocol (with the sonication step) then R2 reads won't "line up" nicely so ipyrad has trouble assembling R2. For pairgbs it should use both R1 and R2 just fine. If it's paired end gbs and r2 is getting ignored then that's a bug.