An automated process for detecting the presence of a target nucleic acid in a sample. The process is performed in a stand-alone unit and includes separating the target nucleic acid from other material present in the sample, engaging a robotic pipettor to combine the separated target nucleic acid and reagents for performing an amplification reaction, and performing an amplification reaction. A product of the amplification reaction is detected as an indication of the presence of the target nucleic acid in the sample.