A system for separating an analyte from other components of a sample includes a receptacle holding station and a magnetic separation station. The receptacle holding station includes one or more stationary, permanent magnets positioned to apply a magnetic field to the contents of a receptacle held stationary within the receptacle holding station. The magnetic separation station includes one or more permanent magnets and is configured to perform a magnetic separation procedure on the contents of a receptacle transported from the receptacle holding station to the magnetic separation station. 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 permanent magnets after the receptacle is transported to the magnetic separation station.