NeSSM: a Next-generation Sequencing Simulator for Metagenomics.
NeSSM: a Next-generation Sequencing Simulator for Metagenomics.
复制标题
NeSSM：下一代宏基因组测序模拟器
DOI：
10.1371/journal.pone.0075448
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Wei C
中科院分区：
文献类型：
--
作者：
Jia B;Xuan L;Cai K;Hu Z;Ma L;Wei C
宏基因组学可以揭示绝大多数被传统的基于培养的方法遗漏的微生物。由于其应用领域非常广泛，具有高保真度的快速宏基因组测序模拟系统的需求非常大，以促进宏基因组学分析工具的开发和比较。我们在这里介绍了一个可定制的宏基因组模拟系统：NeSSM（下一代宏基因组测序模拟器）。结合目前可用的完整基因组，社区组成表和测序参数，它可以比现有系统更好地模拟宏基因组测序。基于每个碱基处的错误的明确分布和测序覆盖偏差的测序错误模型被并入模拟中。为了提高模拟的逼真度，NeSSM提供了直接从现有宏基因组测序数据估计测序误差模型、测序覆盖偏差和群落组成的工具。目前，NeSSM支持454和Illumina平台的单端和双端测序。此外，还开发了NeSSM的GPU（图形处理单元）版本以加速模拟。通过将NeSSM的模拟测序数据与实验宏基因组测序数据进行比较，我们证明了NeSSM在许多方面优于现有流行的宏基因组模拟器，如MetaSim，GemSIM和Grinder。NeSSM的GPU版本比MetaSim快一个数量级以上。NeSSM是用于高通量宏基因组测序的快速模拟系统。它对于开发宏基因组学分析的工具和评估策略很有帮助，学术用户可以在http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php上免费获得它。
Metagenomics can reveal the vast majority of microbes that have been missed by traditional cultivation-based methods. Due to its extremely wide range of application areas, fast metagenome sequencing simulation systems with high fidelity are in great demand to facilitate the development and comparison of metagenomics analysis tools. We present here a customizable metagenome simulation system: NeSSM (Next-generation Sequencing Simulator for Metagenomics). Combining complete genomes currently available, a community composition table, and sequencing parameters, it can simulate metagenome sequencing better than existing systems. Sequencing error models based on the explicit distribution of errors at each base and sequencing coverage bias are incorporated in the simulation. In order to improve the fidelity of simulation, tools are provided by NeSSM to estimate the sequencing error models, sequencing coverage bias and the community composition directly from existing metagenome sequencing data. Currently, NeSSM supports single-end and pair-end sequencing for both 454 and Illumina platforms. In addition, a GPU (graphics processing units) version of NeSSM is also developed to accelerate the simulation. By comparing the simulated sequencing data from NeSSM with experimental metagenome sequencing data, we have demonstrated that NeSSM performs better in many aspects than existing popular metagenome simulators, such as MetaSim, GemSIM and Grinder. The GPU version of NeSSM is more than one-order of magnitude faster than MetaSim. NeSSM is a fast simulation system for high-throughput metagenome sequencing. It can be helpful to develop tools and evaluate strategies for metagenomics analysis and it’s freely available for academic users at http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php.
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影响因子：
3.7
作者：
Mundry M;Bornberg-Bauer E;Sammeth M;Feulner PG
通讯作者：
Feulner PG
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影响因子：
3.7
作者：
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通讯作者：
Wei C
影响因子：
4.4
作者：
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通讯作者：
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影响因子：
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作者：
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通讯作者：
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影响因子：
7
作者：
Li, Ruiqiang;Zhu, Hongmei;Wang, Jun
通讯作者：
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