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The 76-bases error model quality distribution. The plot was created by taking 10000 samples for each read position.

Selecting the quality model

The quality model can be configured using the simulators parameter file. In order to activate quality sampling and sequence errors, set the ERR_FILE parameter to either "76" or "35" to use the build in models. Alternatively you can also specify a file name to load a custom model. In addition, also set FASTA true in the parameter file, and the simulator will output a .fastq file inluding qualities and sequencing error.

Creating a custom model

The flux simulator comes with a model generator that is currently based on GEM mapping files produced by the GEM-Mapper.

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