A nucleic acid assay system includes a holding means that receives a sample and a reagent. A PCR reactor means amplifies the sample and produces an amplified sample. A detection means detects PCR amplicon. A transport means selectively transports the sample and the reagent relative to the holding means, the PCR reactor means, and the detection means. A control means is provided for selectively adding the reagent to the sample, mixing the sample and the reagent, performing PCR amplification, and detecting PCR amplicon. A decontamination means is provided for decontaminating the holding means, the PCR reactor means, and the detection means.
 The United States Government has rights in this invention pursuant to Contract No. W-7405-ENG-48 between the United States Department of Energy and the University of California for the operation of Lawrence Livermore National Laboratory.