FASIM: fragments assembly simulation using biased-sampling model and assembly simulation for microbial genome shotgun sequencing

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Title
FASIM: fragments assembly simulation using biased-sampling model and assembly simulation for microbial genome shotgun sequencing
Author(s)
Cheol-Goo Hur; S Kim; C H Kim; Sung Ho Yoon; Y H In; C Kim; H G Cho
Bibliographic Citation
Journal of Microbiology and Biotechnology, vol. 16, no. 5, pp. 683-688
Publication Year
2006
Abstract
We have developed a program for generating shotgun data sets from known genome sequences. Generation of synthetic data sets by computer program is a useful alternative to real data to which students and researchers have limited access. Uniformly-distributed-sampling clones that were adopted by previous programs cannot account for the real situation where sampled reads tend to come from particular regions of the target genome. To reflect such situation, a probabilistic model for biased sampling distribution was developed by using an experimental data set derived from a microbial genome project. Among the experimental parameters tested (varied fragment or read lengths, chimerism, and sequencing error), the extent of sequencing error was the most critical factor that hampered sequence assembly. We propose that an optimum sequencing strategy employing different insert lengths and redundancy can be established by performing a variety of simulations.
Keyword
fragments assembly simulationgenomesampling modelshotgun sequencingcomputer simulationmicrobial geneticsstatistical model
ISSN
1017-7825
Publisher
Korea Soc-Assoc-Inst
Type
Article
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1. Journal Articles > Journal Articles
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