Proc Int Conf Intell Syst Mol Biol. 1999:202-10.

A dataset generator for whole genome shotgun sequencing.

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Celera Genomics, Rockville, MD 20850, USA. MyersGW@celera.com

Abstract

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.

PMID:: 10786303; [PubMed - indexed for MEDLINE]

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A dataset generator for whole genome shotgun sequencing.

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