1 - Introduction

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 models do not simulate molecular processes on the level of atomes, but represent a collection of deterministic approaches with a minimal set of parameters that is able to 

, 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.