MetaSim: a sequencing simulator for genomics and metagenomics.
MetaSim: a sequencing simulator for genomics and metagenomics.
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Metasim：用于基因组学和元基因组学的测序模拟器。
DOI：
10.1371/journal.pone.0003373
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发表时间：
2008-10-08
期刊：
影响因子：
3.7
通讯作者：
Huson, Daniel H.
中科院分区：
文献类型：
--
作者：
Richter, Daniel C.;Ott, Felix;Auch, Alexander F.;Schmid, Ramona;Huson, Daniel H.
宏基因组学这一新的研究领域为各种以前未分类的生态系统提供了令人兴奋的见解。下一代测序技术正在使公共数据库中的环境数据迅速增加。非常需要专门的软件解决方案和统计方法来处理复杂的宏基因组数据集。为了促进宏基因组工具的开发和改进以及宏基因组项目的规划，我们引入了一个名为MetaSim的测序模拟器。我们的软件可用于生成合成读数集合，反映典型宏基因组数据集的不同分类组成。基于给定基因组的数据库，该程序允许用户通过指定存在于NCBI分类学的不同水平的基因组的数量来设计宏基因组，然后使用许多不同测序技术的模拟来收集来自宏基因组的读数。群体采样器可选地基于源基因组和给定的进化树产生进化序列。MetaSim允许用户模拟单个读取数据集，这些数据集可用作规划测序项目或基准宏基因组软件的标准化测试场景。
The new research field of metagenomics is providing exciting insights into various, previously unclassified ecological systems. Next-generation sequencing technologies are producing a rapid increase of environmental data in public databases. There is great need for specialized software solutions and statistical methods for dealing with complex metagenome data sets. To facilitate the development and improvement of metagenomic tools and the planning of metagenomic projects, we introduce a sequencing simulator called MetaSim. Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a metagenome by specifying the number of genomes present at different levels of the NCBI taxonomy, and then to collect reads from the metagenome using a simulation of a number of different sequencing technologies. A population sampler optionally produces evolved sequences based on source genomes and a given evolutionary tree. MetaSim allows the user to simulate individual read datasets that can be used as standardized test scenarios for planning sequencing projects or for benchmarking metagenomic software.
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影响因子：
3
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Rodriguez-Brito B;Rohwer F;Edwards RA
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