A Dataset Generator for Whole Genome Shotgun Sequencing

Proceedings Of The Seventh International Conference On Intelligent Systems For Molecular Biology

Volume

Proceedings Of The Seventh International Conference On Intelligent Systems For Molecular Biology

Contents

Simulated data sets have been found to be useful in developing software systems because (1) they allow one to study the effect of a particular phenomenon in isolation, and (2) one has complete information about the true solution against which to measure the results of the software. In developing a software suite for assembling a whole human genome shotgun data set, we have developed a simulator, celsim, that permits one to describe and stochastically generate a target DNA sequence with a variety of repeat structures, to further generate polymorphic variants if desired, and to generate a shotgun data set that might be sampled from the target sequence(s). We have found the tool invaluable and quite powerful, yet the design is extremely simple, employing a special type of stochastic grammar.