Abstract: A system for analysis of a sample to aid in diagnosis and/or detection of the presence or absence, and/or the identity of, an analyte in the sample is provided. A cartridge with reagents to isolate nucleic acid from a sample inserted in the cartridge and to amplify the isolated nucleic acid, and an instrument that interacts with the cartridge, together provide a self-contained sample to answer system for detection, identification, differentiation and/or quantification of a target nucleic acid in a sample.