latest version of the Flux Simulator

New Features

  • FLUX-9: Splice Junction extractor. The simulator can extract the sequence of splice junctions — hypothetical and real — from an input annotation, applying a certain intron model.
  • FLUX-8: Command line interface — the simulator can be run in command line mode now. There are 3 flags, "-x" for simulating the expression, "-l" for simulated library construction, and "-s" for simulated sequencing. The graphical user interface can be activated with "-X".
  • FLUX-6: PRO file now contains the abundance of each transcript after sequencing (column 9 and 10).
  • BED file: read name identifiers now comply with the FMRD format.


  • FLUX-4: biases in read sampling
  • FLUX-5: parameter READ_NUMBER 0
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