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Implementing a large genomic project is a demanding task, also from the computer science point of view. Besides collecting many genome samples and sequencing them, there is processing of a huge amount of data at every stage of their production and analysis. Efficient transfer and storage of the data is also an important issue. During the execution of such a project, there is a need to maintain work standards and control quality of the results, which can be difficult if a part of the work is carried out externally. Here, we describe our experience with such data quality analysis on a number of levels - from an obvious check of the quality of the results obtained, to examining consistency of the data at various stages of their processing, to verifying, as far as possible, their compatibility with the data describing the sample.