Abstract Cosmic rays are energetic particles traversing space that bombard Earth’s atmosphere frequently and produce vast particle showers while interacting with air nuclei. The origin and composition of high-energy cosmic rays in the knee region (1015 - 1016 eV) of the cosmic-ray energy spectrum remain unclear despite of novel detection and analysis methods used in various surface and underground experiments. The understanding of the knee has improved from its first detection but still there is notable deviation in results between experiments depending on the used detection methods. The aim of the underground cosmic-ray experiment EMMA (Experiment with Multi-Muon Array) is to shed more light on the origin of the knee. EMMA is based on the idea to measure the lateral shape of high-energy muon component produced in cosmic-ray initiated particle showers on an event-by-event basis, that is, separately for each shower, offering a unique way to study the composition of cosmic rays in the knee region. The present work comprises the design, development and implementation of a comprehensive set of analysis tools for the EMMA experiment. It includes the development of the simulation program to generate realistic event data, the track reconstruction program ETANA to reconstruct hits and tracks in detector stations, the visualisation program EmmaEve to scan events, the graphical monitoring program EmmaDiagnosticsGUI to control the functionality of detectors on-line, the efficiency monitoring program to control chamber efficiencies in three-layer stations and the design of the EMMA database to store reconstruction results. Especially the design and tests of ETANA form the backbone of the present work as its optimised performance is crucial for the analysis of EMMA data. Furthermore, in the present work the influence of rock overburden above EMMA on the properties of high-energy muons is investigated by detailed simulations. The reconstruction of hits in drift chambers is studied with measured data including the estimation of the quality of reconstructed hits, the functionality of hit formation procedure and the influence of afterpulses on hit reconstruction. The validity of simulated data that are generated by the EMMA event generation program is evaluated by comparing simulated and measured data with each other. Finally, synergy benefits between the EMMA and ALICE experiments are discussed, which are both underground experiments but different in nature.