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NeSSM: A Next-Generation Sequencing Simulator for Metagenomics

Author

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  • Ben Jia
  • Liming Xuan
  • Kaiye Cai
  • Zhiqiang Hu
  • Liangxiao Ma
  • Chaochun Wei

Abstract

Background: 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. Results: 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. Conclusions: 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.

Suggested Citation

  • Ben Jia & Liming Xuan & Kaiye Cai & Zhiqiang Hu & Liangxiao Ma & Chaochun Wei, 2013. "NeSSM: A Next-Generation Sequencing Simulator for Metagenomics," PLOS ONE, Public Library of Science, vol. 8(10), pages 1-10, October.
    • Handle: RePEc:plo:pone00:0075448
    DOI: 10.1371/journal.pone.0075448
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    1. Gene W. Tyson & Jarrod Chapman & Philip Hugenholtz & Eric E. Allen & Rachna J. Ram & Paul M. Richardson & Victor V. Solovyev & Edward M. Rubin & Daniel S. Rokhsar & Jillian F. Banfield, 2004. "Community structure and metabolism through reconstruction of microbial genomes from the environment," Nature, Nature, vol. 428(6978), pages 37-43, March.
    2. Marvin Mundry & Erich Bornberg-Bauer & Michael Sammeth & Philine G D Feulner, 2012. "Evaluating Characteristics of De Novo Assembly Software on 454 Transcriptome Data: A Simulation Approach," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-10, February.
    3. Peng Jia & Liming Xuan & Lei Liu & Chaochun Wei, 2011. "MetaBinG: Using GPUs to Accelerate Metagenomic Sequence Classification," PLOS ONE, Public Library of Science, vol. 6(11), pages 1-5, November.
    4. Ravi K Patel & Mukesh Jain, 2012. "NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-7, February.
    5. Marcel Margulies & Michael Egholm & William E. Altman & Said Attiya & Joel S. Bader & Lisa A. Bemben & Jan Berka & Michael S. Braverman & Yi-Ju Chen & Zhoutao Chen & Scott B. Dewell & Lei Du & Joseph , 2005. "Genome sequencing in microfabricated high-density picolitre reactors," Nature, Nature, vol. 437(7057), pages 376-380, September.
    6. Dongying Wu & Philip Hugenholtz & Konstantinos Mavromatis & Rüdiger Pukall & Eileen Dalin & Natalia N. Ivanova & Victor Kunin & Lynne Goodwin & Martin Wu & Brian J. Tindall & Sean D. Hooper & Amrita P, 2009. "A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea," Nature, Nature, vol. 462(7276), pages 1056-1060, December.
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