Standard

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. / Mavromatis, Konstantinos; Barry, Kerrie; Shapiro, Harris; Goltsman, Eugene; McHardy, Alice C.; Rigoutsos, Isidore; Salamov, Asaf; Korzeniewski, Frank; Land, Miriam; Lapidus, Alla; Grigoriev, Igor; Richardson, Paul; Hugenholtz, Philip; Kyrpides, Nikos C.

в: Nature Methods, Том 4, № 6, 06.2007, стр. 495-500.

Результаты исследований: Научные публикации в периодических изданиях › статья › Рецензирование

Harvard

Mavromatis, K, Barry, K, Shapiro, H, Goltsman, E, McHardy, AC, Rigoutsos, I, Salamov, A, Korzeniewski, F, Land, M, Lapidus, A, Grigoriev, I, Richardson, P, Hugenholtz, P & Kyrpides, NC 2007, 'Use of simulated data sets to evaluate the fidelity of metagenomic processing methods', Nature Methods, Том. 4, № 6, стр. 495-500. https://doi.org/10.1038/nmeth1043

APA

Mavromatis, K., Barry, K., Shapiro, H., Goltsman, E., McHardy, A. C., Rigoutsos, I., Salamov, A., Korzeniewski, F., Land, M., Lapidus, A., Grigoriev, I., Richardson, P., Hugenholtz, P., & Kyrpides, N. C. (2007). Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods, 4(6), 495-500. https://doi.org/10.1038/nmeth1043

Vancouver

Mavromatis K, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I и пр. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods. 2007 Июнь;4(6):495-500. https://doi.org/10.1038/nmeth1043

Author

Mavromatis, Konstantinos ; Barry, Kerrie ; Shapiro, Harris ; Goltsman, Eugene ; McHardy, Alice C. ; Rigoutsos, Isidore ; Salamov, Asaf ; Korzeniewski, Frank ; Land, Miriam ; Lapidus, Alla ; Grigoriev, Igor ; Richardson, Paul ; Hugenholtz, Philip ; Kyrpides, Nikos C. / Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. в: Nature Methods. 2007 ; Том 4, № 6. стр. 495-500.

BibTeX

@article{eec811a5a93e4f749702c9a336fc72a3,
title = "Use of simulated data sets to evaluate the fidelity of metagenomic processing methods",
abstract = "Metagenomics is a rapidly emerging field of research for studying microbial communities. To evaluate methods presently used to process metagenomic sequences, we constructed three simulated data sets of varying complexity by combining sequencing reads randomly selected from 113 isolate genomes. These data sets were designed to model real metagenomes in terms of complexity and phylogenetic composition. We assembled sampled reads using three commonly used genome assemblers (Phrap, Arachne and JAZZ), and predicted genes using two popular gene-finding pipelines (fgenesb and CRITICA/GLIMMER). The phylogenetic origins of the assembled contigs were predicted using one sequence similarity-based (blast hit distribution) and two sequence composition-based (PhyloPythia, oligonucleotide frequencies) binning methods. We explored the effects of the simulated community structure and method combinations on the fidelity of each processing step by comparison to the corresponding isolate genomes. The simulated data sets are available online to facilitate standardized benchmarking of tools for metagenomic analysis.Please visit methagora to view and post comments on this article.",
author = "Konstantinos Mavromatis and Kerrie Barry and Harris Shapiro and Eugene Goltsman and McHardy, {Alice C.} and Isidore Rigoutsos and Asaf Salamov and Frank Korzeniewski and Miriam Land and Alla Lapidus and Igor Grigoriev and Paul Richardson and Philip Hugenholtz and Kyrpides, {Nikos C.}",
note = "Funding Information: We thank A. Lykidis and I. Anderson from the Genome Biology Program at DOE-JGI for their feedback and comments on this manuscript. This work was performed under the auspices of the US Department of Energy{\textquoteright}s Office of Science, Biological and Environmental Research Program, and the University of California, Lawrence Livermore National Laboratory under contract number W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract number DE-AC02-05CH11231 and Los Alamos National Laboratory under contract number W-7405-ENG-36.",
year = "2007",
month = jun,
doi = "10.1038/nmeth1043",
language = "English",
volume = "4",
pages = "495--500",
journal = "Nature Methods",
issn = "1548-7091",
publisher = "Nature Publishing Group",
number = "6",

}

RIS

TY - JOUR

T1 - Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

AU - Mavromatis, Konstantinos

AU - Barry, Kerrie

AU - Shapiro, Harris

AU - Goltsman, Eugene

AU - McHardy, Alice C.

AU - Rigoutsos, Isidore

AU - Salamov, Asaf

AU - Korzeniewski, Frank

AU - Land, Miriam

AU - Lapidus, Alla

AU - Grigoriev, Igor

AU - Richardson, Paul

AU - Hugenholtz, Philip

AU - Kyrpides, Nikos C.

N1 - Funding Information: We thank A. Lykidis and I. Anderson from the Genome Biology Program at DOE-JGI for their feedback and comments on this manuscript. This work was performed under the auspices of the US Department of Energy’s Office of Science, Biological and Environmental Research Program, and the University of California, Lawrence Livermore National Laboratory under contract number W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract number DE-AC02-05CH11231 and Los Alamos National Laboratory under contract number W-7405-ENG-36.

PY - 2007/6

Y1 - 2007/6

N2 - Metagenomics is a rapidly emerging field of research for studying microbial communities. To evaluate methods presently used to process metagenomic sequences, we constructed three simulated data sets of varying complexity by combining sequencing reads randomly selected from 113 isolate genomes. These data sets were designed to model real metagenomes in terms of complexity and phylogenetic composition. We assembled sampled reads using three commonly used genome assemblers (Phrap, Arachne and JAZZ), and predicted genes using two popular gene-finding pipelines (fgenesb and CRITICA/GLIMMER). The phylogenetic origins of the assembled contigs were predicted using one sequence similarity-based (blast hit distribution) and two sequence composition-based (PhyloPythia, oligonucleotide frequencies) binning methods. We explored the effects of the simulated community structure and method combinations on the fidelity of each processing step by comparison to the corresponding isolate genomes. The simulated data sets are available online to facilitate standardized benchmarking of tools for metagenomic analysis.Please visit methagora to view and post comments on this article.

AB - Metagenomics is a rapidly emerging field of research for studying microbial communities. To evaluate methods presently used to process metagenomic sequences, we constructed three simulated data sets of varying complexity by combining sequencing reads randomly selected from 113 isolate genomes. These data sets were designed to model real metagenomes in terms of complexity and phylogenetic composition. We assembled sampled reads using three commonly used genome assemblers (Phrap, Arachne and JAZZ), and predicted genes using two popular gene-finding pipelines (fgenesb and CRITICA/GLIMMER). The phylogenetic origins of the assembled contigs were predicted using one sequence similarity-based (blast hit distribution) and two sequence composition-based (PhyloPythia, oligonucleotide frequencies) binning methods. We explored the effects of the simulated community structure and method combinations on the fidelity of each processing step by comparison to the corresponding isolate genomes. The simulated data sets are available online to facilitate standardized benchmarking of tools for metagenomic analysis.Please visit methagora to view and post comments on this article.

UR - http://www.scopus.com/inward/record.url?scp=34249794257&partnerID=8YFLogxK

U2 - 10.1038/nmeth1043

DO - 10.1038/nmeth1043

M3 - Article

C2 - 17468765

AN - SCOPUS:34249794257

VL - 4

SP - 495

EP - 500

JO - Nature Methods

JF - Nature Methods

SN - 1548-7091

IS - 6

ER -

ID: 90036674