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Many software tools are currently available to solve the hard goal of assembling millions of fragments produced in sequencing projects. Such a variety includes packages for long and short reads, generated by classical and next-generation sequencing technologies. Often the result produced by different tools can diverge-sometime significantly-for many reasons: the underlying algorithm, the data structures employed, the heuristics implemented, default parameters, etc. On the ground of the above considerations, we were motivated in developing a methodology which may both guide in a comparison of different assembler's output and improve the overall quality of the genome assembly sequences,by merging the sequences produced by different assembly programs.