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The Flux Simulator aims at modeling RNA-Seq experiments in silico: sequencing reads are produced from a reference genome according annotated transcripts. The simulation pipeline models different steps as modules, each with a minimal set of parameters that can be estimated by experimental parameters. These  The first step is-in fact-a transcriptome simulator. Subsequently, common sources of systematic bias in the abundance and distribution of produced reads are simulated by in silico library preparation and sequencing. Our models do not simulate molecular processes on the level of atomesatoms, but represent a collection of deterministic approaches with a minimal set of parameters that can be estimated from observations of the experiment that is to be reproduced.