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GALAPAGOS, Galaxy Analysis over Large Areas: Parameter Assessment by GALFITting Objects from SExtractor (ascl:1010.064), automates source detection, two-dimensional light-profile Sersic modelling and catalogue compilation in large survey applications. Based on a single setup, GALAPAGOS can process a complete set of survey images. It detects sources in the data, estimates a local sky background, cuts postage stamp images for all sources, prepares object masks, performs Sersic fitting including neighbours and compiles all objects in a final output catalogue. For the initial source detection GALAPAGOS applies SExtractor, while GALFIT (ascl:1104.010) is incorporated for modelling Sersic profiles. It measures the background sky involved in the Sersic fitting by means of a flux growth curve. GALAPAGOS determines postage stamp sizes based on SExtractor shape parameters. In order to obtain precise model parameters GALAPAGOS incorporates a complex sorting mechanism and makes use of multiplexing capabilities. It combines SExtractor and GALFIT data in a single output table. When incorporating information from overlapping tiles, GALAPAGOS automatically removes multiple entries from identical sources. GALAPAGOS is programmed in the Interactive Data Language, IDL. A C implementation of the software, GALAPAGOS-C (ascl:1408.011), is available.