The Cherenkov Telescope Array (CTA) will be able to perform unprecedented observations of the transient very high-energy sky. An on-line science alert generation (SAG) pipeline, with a required 30 second latency, will allow the discovery or follow-up of gamma ray bursts (GRBs) and flaring emission from active galactic nuclei, galactic compact objects and electromagnetic counterparts of gravitational waves or neutrino messengers. The CTA sensitivity for very short exposures does not only depend on the technological performance of the array (e.g. effective area, background discrimination efficiency). The algorithms to evaluate the significance of the detection also define the sensitivity, together with their computational efficiency in order to satisfy the SAG latency requirements. We explore the aperture photometry and likelihood analysis techniques, and the associated parameters (e.g. on-source to off-source exposure ratio, minimum number of required signal events), defining the CTA ability to detect a significant signal at short exposures. The resulting CTA differential flux sensitivity as a function of the observing time, obtained using the latest Monte Carlo simulations, is compared to the sensitivities of Fermi-LAT and current-generation IACTs obtained in the overlapping energy ranges.
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