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Volumn 30, Issue 5, 2014, Pages 629-635

Nonpareil: A redundancy-based approach to assess the level of coverage in metagenomic datasets

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; METAGENOME; METAGENOMICS; METHODOLOGY; MICROBIOLOGY; MICROFLORA;

EID: 84897693692     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt584     Document Type: Article
Times cited : (171)

References (34)
  • 1
    • 84875609855 scopus 로고    scopus 로고
    • Filtering duplicate reads from 454 pyrosequencing data
    • Balzer,S. et al. (2013) Filtering duplicate reads from 454 pyrosequencing data. Bioinformatics, 29, 830-836.
    • (2013) Bioinformatics , vol.29 , pp. 830-836
    • Balzer, S.1
  • 2
    • 0031722856 scopus 로고    scopus 로고
    • Analysis of the quality and utility of random shotgun sequencing at low redundancies
    • Bouck,J. et al. (1998) Analysis of the quality and utility of random shotgun sequencing at low redundancies. Genome Res., 8, 1074-1084.
    • (1998) Genome Res. , vol.8 , pp. 1074-1084
    • Bouck, J.1
  • 3
    • 77952243141 scopus 로고    scopus 로고
    • QIIME allows analysis of high-throughput community sequencing data
    • Caporaso,J.G. et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat. Methods, 7, 335-336.
    • (2010) Nat. Methods , vol.7 , pp. 335-336
    • Caporaso, J.G.1
  • 5
    • 0001463548 scopus 로고
    • Nonparametric estimation of the number of classes in a population
    • Chao,A. (1984) Nonparametric estimation of the number of classes in a population. Scand. J. Stat., 11, 265-270.
    • (1984) Scand. J. Stat. , vol.11 , pp. 265-270
    • Chao, A.1
  • 6
    • 77957151956 scopus 로고    scopus 로고
    • SolexaQA: At-A-Glance quality assessment of Illumina secondgeneration sequencing data
    • Cox,M.P. et al. (2010) SolexaQA: at-a-glance quality assessment of Illumina secondgeneration sequencing data. BMC Bioinformatics, 11, 485.
    • (2010) BMC Bioinformatics , vol.11 , pp. 485
    • Cox, M.P.1
  • 7
    • 84875700725 scopus 로고    scopus 로고
    • Predicting the molecular complexity of sequencing libraries
    • Daley,T. and Smith,A.D. (2013) Predicting the molecular complexity of sequencing libraries. Nat. Methods, 10, 325-327.
    • (2013) Nat. Methods , vol.10 , pp. 325-327
    • Daley, T.1    Smith, A.D.2
  • 8
    • 84860160394 scopus 로고    scopus 로고
    • In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids
    • Denef,V.J. and Banfield,J.F. (2012) In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids. Science, 336, 462-466.
    • (2012) Science , vol.336 , pp. 462-466
    • Denef, V.J.1    Banfield, J.F.2
  • 9
    • 0019610360 scopus 로고
    • An adaptive nonlinear least-squares algorithm
    • Dennis,J.E. et al. (1981) An adaptive nonlinear least-squares algorithm. ACM Trans. Math. Softw., 7, 348-368.
    • (1981) ACM Trans. Math. Softw. , vol.7 , pp. 348-368
    • Dennis, J.E.1
  • 10
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from highthroughput DNA sequencing
    • Dohm,J.C. et al. (2008) Substantial biases in ultra-short read data sets from highthroughput DNA sequencing. Nucleic Acids Res., 36, e105.
    • (2008) Nucleic Acids Res. , vol.36
    • Dohm, J.C.1
  • 11
    • 0000760438 scopus 로고
    • The efficiency of good's nonparametric coverage estimator
    • Esty,W.W. (1986) The efficiency of good's nonparametric coverage estimator. Ann. Stat., 14, 1257-1260.
    • (1986) Ann. Stat. , vol.14 , pp. 1257-1260
    • Esty, W.W.1
  • 12
    • 84871826193 scopus 로고    scopus 로고
    • Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
    • Fierer,N. et al. (2012) Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc. Natl Acad. Sci. USA, 109, 21390-21395.
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 21390-21395
    • Fierer, N.1
  • 13
    • 0000803388 scopus 로고
    • The population frequencies of species and the estimation of population parameters
    • Good,I.J. (1953) The population frequencies of species and the estimation of population parameters. Biometrika, 40, 237-264.
    • (1953) Biometrika , vol.40 , pp. 237-264
    • Good, I.J.1
  • 14
    • 33846555715 scopus 로고    scopus 로고
    • DNA-DNA hybridization values and their relationship to whole-genome sequence similarities
    • Goris,J. et al. (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol., 57, 81-91.
    • (2007) Int. J. Syst. Evol. Microbiol. , vol.57 , pp. 81-91
    • Goris, J.1
  • 15
    • 77949524553 scopus 로고    scopus 로고
    • Estimating DNA coverage and abundance in metagenomes using a gamma approximation
    • Hooper,S.D. et al. (2010) Estimating DNA coverage and abundance in metagenomes using a gamma approximation. Bioinformatics, 26, 295-301.
    • (2010) Bioinformatics , vol.26 , pp. 295-301
    • Hooper, S.D.1
  • 16
    • 0035487318 scopus 로고    scopus 로고
    • Counting the uncountable: Statistical approaches to estimating microbial diversity
    • Hughes,J.B. et al. (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol., 67, 4399-4406.
    • (2001) Appl. Environ. Microbiol. , vol.67 , pp. 4399-4406
    • Hughes, J.B.1
  • 17
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • HumanMicrobiome Project Consortium
    • HumanMicrobiome Project Consortium. (2012) Structure, function and diversity of the healthy human microbiome. Nature, 486, 207-214.
    • (2012) Nature , vol.486 , pp. 207-214
  • 18
    • 35748954014 scopus 로고    scopus 로고
    • Prokaryotic taxonomy and phylogeny in the genomic era: Advancements and challenges ahead
    • Konstantinidis,K.T. and Tiedje,J.M. (2007) Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr. Opin. Microbiol., 10, 504-509.
    • (2007) Curr. Opin. Microbiol. , vol.10 , pp. 504-509
    • Konstantinidis, K.T.1    Tiedje, J.M.2
  • 19
    • 62549131646 scopus 로고    scopus 로고
    • PEMer: A computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
    • Korbel,J.O. et al. (2009) PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol., 10, R23.
    • (2009) Genome Biol. , vol.10
    • Korbel, J.O.1
  • 20
    • 73349110099 scopus 로고    scopus 로고
    • Wrinkles in the rare biosphere: Pyrosequencing errors can lead to artificial inflation of diversity estimates
    • Kunin,V. et al. (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ. Microbiol., 12, 118-123.
    • (2010) Environ. Microbiol. , vol.12 , pp. 118-123
    • Kunin, V.1
  • 21
    • 0023988195 scopus 로고
    • Genomic mapping by fingerprinting random clones: A mathematical analysis
    • Lander,E.S. and Waterman,M.S. (1988) Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics, 2, 231-239.
    • (1988) Genomics , vol.2 , pp. 231-239
    • Lander, E.S.1    Waterman, M.S.2
  • 22
    • 84871780204 scopus 로고    scopus 로고
    • Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms
    • Liu,J. et al. (2013) Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms. Nucleic Acids Res., 41, e3.
    • (2013) Nucleic Acids Res. , vol.41
    • Liu, J.1
  • 23
    • 83555174830 scopus 로고    scopus 로고
    • Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw
    • Mackelprang,R. et al. (2011) Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature, 480, 368-371.
    • (2011) Nature , vol.480 , pp. 368-371
    • Mackelprang, R.1
  • 24
    • 80052753042 scopus 로고    scopus 로고
    • Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem
    • Oh,S. et al. (2011) Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem. Appl. Environ. Microbiol., 77, 6000-6011.
    • (2011) Appl. Environ. Microbiol. , vol.77 , pp. 6000-6011
    • Oh, S.1
  • 25
    • 79952750340 scopus 로고    scopus 로고
    • Vaginal microbiome of reproductive-age women
    • Ravel,J. et al. (2011) Vaginal microbiome of reproductive-age women. Proc. Natl Acad. Sci. USA, 108 (Suppl. 1), 4680-4687.
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , Issue.SUPPL. 1 , pp. 4680-4687
    • Ravel, J.1
  • 26
    • 10944226351 scopus 로고    scopus 로고
    • Metagenomics: Genomic analysis of microbial communities
    • Riesenfeld,C.S. et al. (2004) Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet., 38, 525-552.
    • (2004) Annu. Rev. Genet. , vol.38 , pp. 525-552
    • Riesenfeld, C.S.1
  • 27
    • 39049092823 scopus 로고    scopus 로고
    • A statistical toolbox for metagenomics: Assessing functional diversity in microbial communities
    • Schloss,P.D. and Handelsman,J. (2008) A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. BMC Bioinformatics, 9, 34.
    • (2008) BMC Bioinformatics , vol.9 , pp. 34
    • Schloss, P.D.1    Handelsman, J.2
  • 28
    • 72949107142 scopus 로고    scopus 로고
    • Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
    • Schloss,P.D. et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol., 75, 7537-7541.
    • (2009) Appl. Environ. Microbiol. , vol.75 , pp. 7537-7541
    • Schloss, P.D.1
  • 29
    • 77955631533 scopus 로고    scopus 로고
    • Occupancy modeling, maximum contig size probabilities and designing metagenomics experiments
    • Stanhope,S.A. (2010) Occupancy modeling, maximum contig size probabilities and designing metagenomics experiments. PLoS One, 5, e11652.
    • (2010) PLoS One , vol.5
    • Stanhope, S.A.1
  • 30
    • 84860855706 scopus 로고    scopus 로고
    • COVER: A priori estimation of coverage for metagenomic sequencing
    • Tamames,J. et al. (2012) COVER: a priori estimation of coverage for metagenomic sequencing. Environ. Microbiol. Rep., 4, 335-341.
    • (2012) Environ. Microbiol. Rep. , vol.4 , pp. 335-341
    • Tamames, J.1
  • 31
    • 84874536596 scopus 로고    scopus 로고
    • The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses
    • Vetrovský.T. and Baldrian,P. (2013) The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS One, 8, e57923.
    • (2013) PLoS One , vol.8
    • Vetrovský, T.1    Baldrian, P.2
  • 32
    • 33749242769 scopus 로고    scopus 로고
    • A general coverage theory for shotgun DNA sequencing
    • Wendl,M.C. (2006) A general coverage theory for shotgun DNA sequencing. J. Comput. Biol., 13, 1177-1196.
    • (2006) J. Comput. Biol. , vol.13 , pp. 1177-1196
    • Wendl, M.C.1
  • 33
    • 84885381231 scopus 로고    scopus 로고
    • Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem
    • Wendl,M.C. et al. (2012) Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem. J. Math. Biol., 67, 1141-1161.
    • (2012) J. Math. Biol. , vol.67 , pp. 1141-1161
    • Wendl, M.C.1
  • 34
    • 72949101201 scopus 로고    scopus 로고
    • A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
    • Wu,D. et al. (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462, 1056-1060.
    • (2009) Nature , vol.462 , pp. 1056-1060
    • Wu, D.1


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