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The Flux Simulator aims at reproducing in silico the experimental pipelines of RNA-Seq experiments. , adopting a minimal set of parameters. Corresponding models were established after analyzing RNA-Seq experiments from different cell types, sample preparation protocols and sequencing platforms. The first step of the FLUX project is-in fact-a transcriptome simulator. Subsequently, common sources of systematic bias in the abundance and distribution of produced reads are mimicked-whether they incur during library construction, or, in thesequencing process. The FluxSimulator provides a flexible base to design benchmarkexperiments based on the new sequencing technologies, as for instance abundance predictions of the FluxCapacitor.