NeSSM: a Next-generation Sequencing Simulator for Metagenomics.

<h4>Background</h4>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 facilitat...

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Autores principales:	Ben Jia, Liming Xuan, Kaiye Cai, Zhiqiang Hu, Liangxiao Ma, Chaochun Wei
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2d619a9df3e042acac44389399a1d6cf
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spelling	oai:doaj.org-article:2d619a9df3e042acac44389399a1d6cf2021-11-18T08:52:30ZNeSSM: a Next-generation Sequencing Simulator for Metagenomics.1932-620310.1371/journal.pone.0075448https://doaj.org/article/2d619a9df3e042acac44389399a1d6cf2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24124490/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>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.<h4>Results</h4>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.<h4>Conclusions</h4>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.Ben JiaLiming XuanKaiye CaiZhiqiang HuLiangxiao MaChaochun WeiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 10, p e75448 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ben Jia Liming Xuan Kaiye Cai Zhiqiang Hu Liangxiao Ma Chaochun Wei NeSSM: a Next-generation Sequencing Simulator for Metagenomics.
description	<h4>Background</h4>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.<h4>Results</h4>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.<h4>Conclusions</h4>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.
format	article
author	Ben Jia Liming Xuan Kaiye Cai Zhiqiang Hu Liangxiao Ma Chaochun Wei
author_facet	Ben Jia Liming Xuan Kaiye Cai Zhiqiang Hu Liangxiao Ma Chaochun Wei
author_sort	Ben Jia
title	NeSSM: a Next-generation Sequencing Simulator for Metagenomics.
title_short	NeSSM: a Next-generation Sequencing Simulator for Metagenomics.
title_full	NeSSM: a Next-generation Sequencing Simulator for Metagenomics.
title_fullStr	NeSSM: a Next-generation Sequencing Simulator for Metagenomics.
title_full_unstemmed	NeSSM: a Next-generation Sequencing Simulator for Metagenomics.
title_sort	nessm: a next-generation sequencing simulator for metagenomics.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/2d619a9df3e042acac44389399a1d6cf
work_keys_str_mv	AT benjia nessmanextgenerationsequencingsimulatorformetagenomics AT limingxuan nessmanextgenerationsequencingsimulatorformetagenomics AT kaiyecai nessmanextgenerationsequencingsimulatorformetagenomics AT zhiqianghu nessmanextgenerationsequencingsimulatorformetagenomics AT liangxiaoma nessmanextgenerationsequencingsimulatorformetagenomics AT chaochunwei nessmanextgenerationsequencingsimulatorformetagenomics
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NeSSM: a Next-generation Sequencing Simulator for Metagenomics.

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