PyroSim is a simulator for pyrosequencing.

It currently supports Roche 454 sequencing, and attempts to model
accurately the flowgram generation, including base and quality
calling.  The output is written as an SFF file.

Currently, only the original GS20 generation is supported, but the
newer FLX and Titanium generations should be easy to add, as soon as
we have reasonably accurate statistical models for the flow
distributions, and a better idea of how to do quality calling.

(For GS20, the called quality depends only on the flow value, so it is
reverse-engineered and implemented using a lookup table)

Usage is:

   pyrosim [-G gen] [-n count] [-f flows] [<input.fasta>] 

where 'gen' may currently be only GS20, -n specifies the number of
reads to generate, and <input.fasta> is the name of a fasta file
containing the sequence to simulate reads from (e.g. a genome).

Currently, only the first sequence in the input is used.

If you are interested in using this, or in further development, please
contact me at ketil dot malde at imr dot no.