A dataset generator for whole genome shotgun sequencing.
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.
Myers
G
G
Celera Genomics, Rockville, MD 20850, USA. MyersGW@celera.com
D001483:Base Sequence; D003198:Computer Simulation; D016208:Databases, Factual; D015894:Genome, Human; D006239:Haplotypes; D006801:Humans; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software