The definition of the library kit in the plan run is optional. At the moment, there is an option for the CEPH library control and you can leave that field blank. The two parameters that are important for the control libraries are: the correct amount of flows (500 for 200 bp libraries or 850 for 400 bp libraries) and the correct reference (hg19 for CEPH and E. coli DH10B for E. coli).
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.