This option is up to the user. Using an on-deck thermocycler provides a higher level of automation compared to an off-deck thermocycler. However, both options will require manual interventions. The use of on-deck thermocyclers may not be possible with all instrument types, and this must also be specified in the automation script protocol.
If a stand-alone thermocycler is available in a comfortable vicinity of the robot, we can suggest to use an off-deck thermocycler for steps 2 – 3, and step 4, as conventional thermocyclers provide heated lid options that prevent condensation. Depending on the type of on-deck thermocycler used, a heated lid option may not be provided.
The current Perkin Elmer Sciclone, Eppendorf EpMotion 5075, Hamilton STAR / STARlet / NGS STAR, and Agilent Bravo Workstation (B) protocols are setup for off-deck thermocyclers. The current Beckman Coulter Biomek FxP / i7 protocols are written for on-deck thermocycling at all steps, including the PCR. However, modifications to all protocols can be made in collaboration with the respective liquid handler manufacturer.
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