9.3.2.3. Detection chemistry

There are many different detection chemistries available for following qPCR in real-time (de Miranda, 2008). The two most common are SYBR-green and similar DNA-binding dyes, and fluorophore-labelled hydrolysis (TaqMan) probes. The merits of both systems are discussed in the BEEBOOK paper on molecular methods (Evans et al., 2013). TaqMan assays are best suited for well-optimized, stable assays for widespread, routine diagnosis. SYBR-green assays are better suited for discovery, characterization of new strains and analysis of strain mixtures (Papin et al., 2004). They are also much cheaper to design, adapt and optimize (Bustin and Nolan, 2004).