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The Flux Simulator supports quality error models to simulate sequencing errors. The current version of the Flux Simulator provides two models, one for reads of length 76 and one for read length 36, but the model generator is included and allows the creation of custom models. In the current version, the Flux Simulator error models can not be used for longer read length, but we are working on a solution to support also longer reads with the current models (
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Applying the error model consists of two steps. First, a quality value is assigned to each position in the read. Second, a cross-talk table is used to check if the base with the given quality should be mutated and if so, to which base. The quality assignment is based on a Markov model that uses both the position n in the read and the quality value of the n-1 positions.
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We are also working on an implementation of the model generator that works with SAM files (
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