A cartridge assembly, comprising: a housing (101, 102) that includes an illumination chamber and a well plate, the well plate maintained within the housing (101, 102) and having liquid wells (154, 156) to receive desired amounts of liquids, the well plate including a fluidics analysis station aligned with the illumination chamber, the well plate including an interface window and interface ports (180, 182) located at the fluidics analysis station, the well plate including a valve station and pump station, the well plate including channels associated with the wells, the valve station, pump station and fluidics analysis station, the wells (154, 156) each having a cover; a pump assembly provided on the well plate at the pump station, the pump assembly to manage fluid flow through the channels between the pump station and the fluidics analysis station; the housing (101, 102) including a flow cell chamber to receive a flow cell cartridge, the cartridge assembly further comprising a flow cell cartridge having a frame (904, 906) that contains an analysis circuit therein, the frame (904, 906) including a flow cell window aligned with the analysis circuit, the frame (904, 906) including flow cell ports that are fluidly coupled to an active area _in the analysis circuit, the flow cell chamber to position the flow cell cartridge at the fluidics analysis station with the flow cell window and ports aligned with the corresponding interface window and ports (180, 182), respectively characterised in that, the cartridge assembly comprises, a piercer unit provided in the housing (101, 102) and positioned proximate to the wells (154, 156), wherein the piercer unit includes a body that is shaped in a conical tubular manner with a lower platform, an intermediate segment and an upper flange, at least one of the lower platform or the upper flange comprising piercing elements (312, 314) distributed in a predetermined manner, the piercing elements (312, 314) arranged to align with the wells on the well plate., the piercer unit to be moved to a piercing position where the piercing elements (312, 314) pierce the covers for the corresponding wells (154, 156), and a rotary valve assembly on the well plate at the valve station, the rotary valve assembly having a rotor shaft and rotor valve positioned to rotate about a rotational axis and to selectively couple the wells to the pump station, the rotor shaft having a distal end exposed through the housing, including a dual spline configuration at the distal end thereof, the dual spline configuration having first and second sets of splines, the first set of splines forming a drive interface, the second set of splines forming a position encoding interface. a housing (101, 102) that includes an illumination chamber and a well plate, the well plate maintained within the housing (101, 102) and having liquid wells (154, 156) to receive desired amounts of liquids, the well plate including a fluidics analysis station aligned with the illumination chamber, the well plate including an interface window and interface ports (180, 182) located at the fluidics analysis station, the well plate including a valve station and pump station, the well plate including channels associated with the wells, the valve station, pump station and fluidics analysis station, the wells (154, 156) each having a cover; a pump assembly provided on the well plate at the pump station, the pump assembly to manage fluid flow through the channels between the pump station and the fluidics analysis station; the housing (101, 102) including a flow cell chamber to receive a flow cell cartridge, the cartridge assembly further comprising a flow cell cartridge having a frame (904, 906) that contains an analysis circuit therein, the frame (904, 906) including a flow cell window aligned with the analysis circuit, the frame (904, 906) including flow cell ports that are fluidly coupled to an active area _in the analysis circuit, the flow cell chamber to position the flow cell cartridge at the fluidics analysis station with the flow cell window and ports aligned with the corresponding interface window and ports (180, 182), respectively characterised in that, the cartridge assembly comprises, a piercer unit provided in the housing (101, 102) and positioned proximate to the wells (154, 156), wherein the piercer unit includes a body that is shaped in a conical tubular manner with a lower platform, an intermediate segment and an upper flange, at least one of the lower platform or the upper flange comprising piercing elements (312, 314) distributed in a predetermined manner, the piercing elements (312, 314) arranged to align with the wells on the well plate., the piercer unit to be moved to a piercing position where the piercing elements (312, 314) pierce the covers for the corresponding wells (154, 156), and a rotary valve assembly on the well plate at the valve station, the rotary valve assembly having a rotor shaft and rotor valve positioned to rotate about a rotational axis and to selectively couple the wells to the pump station, the rotor shaft having a distal end exposed through the housing, including a dual spline configuration at the distal end thereof, the dual spline configuration having first and second sets of splines, the first set of splines forming a drive interface, the second set of splines forming a position encoding interface.