Components of the FlowSim pipeline. For a typical 454 sequencing simulation application, first the clonesim component takes a FASTA-formatted input genome and extracts random fragments representing the clones to be sequenced. The user can specify the statistical distribution to use for clone lengths. gelfilter then simulates filtering by sequence length (i.e. molecule size). kitsim simulates the attachment of 454-specific adapters, synthetic sequence fragments that are used in the sequencing process. mutator introduces random substitutions and indels into sequences. duplicator randomly increases the multiplicity of sequences, simulating the artificial duplicates that occur with most second generation technologies. Finally, flowsim simulates the 454 pyrosequencing process, and generates the final SFF file.