A system for separating an analyte from other components of a sample contained in a receptacle, where the system includes a receptacle holding station and a magnetic separation station. The receptacle holding station is configured to receive and hold a receptacle and includes one or more magnets positioned to apply a magnetic field to the contents of the receptacle. When present in the receptacle holding station, a receptacle remains stationary relative to the one or more magnets. The magnetic separation station includes one or more magnets and is constructed and arranged to perform a magnetic separation procedure on the contents of a receptacle transported from the receptacle holding station to the magnetic separation station by an automated receptacle transport. The magnetic separation procedure includes isolating an analyte immobilized on a magnetically-responsive solid support within the receptacle and removing other components of the sample from the receptacle. The magnetic separation station is configured to provide relative movement between the receptacle and the one or more magnets after the receptacle is transported to the magnetic separation station.