SimCT generates simulated datasets that get as close as possible to specific real biological conditions together with the list of genomic incidents and mutations that have been inserted.

Source code

SimCT source code

Plugin

It is possible to enhance SimCT thanks to its modular architecture.

Let’s consider an example where one would like to replace FluxSimulator (the read simulator we use) by another read simulator. In such a case one should follow this example.

More precisely, the new simulator should derive from CracTools::SimCT::ReadSimulator and define a _generateSimulation function. This function is given the simulated genome in parameter. Another package must be defined, deriving from CracTools::SimCT::ReadSimulation. It has to define three iterators to access, for each read, to: 1. Their genomic intervals (getGenomicIntervalsIterator) 2. Their DNA sequence (getSequenceIterator) 3. Their sequence quality (getErrorsPosIterator)