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Volumn 33, Issue 6, 2017, Pages 791-798

COCACOLA: Binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BACTERIAL GENOME; BACTERIUM; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; METAGENOMICS; MICROFLORA; PROCEDURES; SOFTWARE;

EID: 85018348728     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw290     Document Type: Article
Times cited : (124)

References (45)
  • 1
    • 84879678051 scopus 로고    scopus 로고
    • Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
    • Albertsen, M. et al. (2013) Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat. Biotechnol., 31, 533-538.
    • (2013) Nat. Biotechnol , vol.31 , pp. 533-538
    • Albertsen, M.1
  • 2
    • 84908597294 scopus 로고    scopus 로고
    • Binning metagenomic contigs by coverage and composition
    • Alneberg, J. et al. (2014) Binning metagenomic contigs by coverage and composition. Nat. Methods, 11, 1144-1146.
    • (2014) Nat. Methods , vol.11 , pp. 1144-1146
    • Alneberg, J.1
  • 3
    • 84861180216 scopus 로고    scopus 로고
    • Joint analysis of multiple metagenomic samples
    • Baran, Y. and Halperin, E. (2012) Joint analysis of multiple metagenomic samples. PLoS Comput. Biol., 8, e1002373.
    • (2012) PLoS Comput. Biol. , vol.8 , pp. e1002373
    • Baran, Y.1    Halperin, E.2
  • 5
    • 69549135124 scopus 로고    scopus 로고
    • Phymm and PhymmBL: Metagenomic phylogenetic classification with interpolated Markov models
    • Brady, A. and Salzberg, S.L. (2009) Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat. Methods, 6, 673-676.
    • (2009) Nat. Methods , vol.6 , pp. 673-676
    • Brady, A.1    Salzberg, S.L.2
  • 7
    • 79959532395 scopus 로고    scopus 로고
    • Graph regularized nonnegative matrix factorization for data representation
    • Cai, D. et al. (2011) Graph regularized nonnegative matrix factorization for data representation. IEEE Trans. Pattern Anal. Mach. Intell., 33, 1548-1560.
    • (2011) IEEE Trans. Pattern Anal. Mach. Intell. , vol.33 , pp. 1548-1560
    • Cai, D.1
  • 8
    • 84887265124 scopus 로고    scopus 로고
    • Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution
    • Carr, R. et al. (2013) Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution. PLoS Comput. Biol., 9, e1003292.
    • (2013) PLoS Comput. Biol. , vol.9 , pp. e1003292
    • Carr, R.1
  • 9
    • 47249139915 scopus 로고    scopus 로고
    • Compostbin: A DNA composition-based algorithm for binning environmental shotgun reads
    • Chatterji, S. et al. (2008) Compostbin: a DNA composition-based algorithm for binning environmental shotgun reads. Res. Comput. Mol. Biol., 17-28.
    • (2008) Res. Comput. Mol. Biol. , pp. 17-28
    • Chatterji, S.1
  • 10
    • 0003882879 scopus 로고    scopus 로고
    • American Mathematical Society
    • Chung, F.R. (1997). Spectral Graph Theory, Vol. 92. American Mathematical Society.
    • (1997) Spectral Graph Theory , vol.92
    • Chung, F.R.1
  • 11
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • Consortium, H.M.P. et al. (2012) Structure, function and diversity of the healthy human microbiome. Nature, 486, 207-214.
    • (2012) Nature , vol.486 , pp. 207-214
    • Consortium, H.M.P.1
  • 12
    • 4043061882 scopus 로고    scopus 로고
    • Variational Bayesian model selection for mixture distributions
    • Key West, Florida, USA
    • Corduneanu, A. and Bishop, CM. (2001) Variational Bayesian model selection for mixture distributions. In: Artificial intelligence and Statistics 2001, Key West, Florida, USA, pp. 27-34.
    • (2001) Artificial Intelligence and Statistics 2001 , pp. 27-34
    • Corduneanu, A.1    Bishop, C.M.2
  • 14
    • 33847702910 scopus 로고    scopus 로고
    • MEGAN analysis of metagenomic data
    • Huson, D.H. et al. (2007) MEGAN analysis of metagenomic data. Genome Res., 17, 377-386.
    • (2007) Genome Res. , vol.17 , pp. 377-386
    • Huson, D.H.1
  • 16
    • 84907682734 scopus 로고    scopus 로고
    • GroopM: An automated tool for the recovery of population genomes from related metagenomes
    • Imelfort, M. et al. (2014) GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ, 2, e603.
    • (2014) PeerJ , vol.2 , pp. e603
    • Imelfort, M.1
  • 17
    • 84914115869 scopus 로고    scopus 로고
    • A clustering approach to constrained binary matrix factorization
    • Springer-Verlag, Berlin Heidelberg
    • Jiang, P. et al. (2014) A clustering approach to constrained binary matrix factorization. In: Data Mining and Knowledge Discovery for Big Data, Springer-Verlag, Berlin Heidelberg, pp. 281-303.
    • (2014) Data Mining and Knowledge Discovery for Big Data , pp. 281-303
    • Jiang, P.1
  • 18
    • 84940387197 scopus 로고    scopus 로고
    • Meta BAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
    • Kang, D.D. et al. (2015) Meta BAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ, 3, e1165.
    • (2015) PeerJ , vol.3 , pp. e1165
    • Kang, D.D.1
  • 19
    • 77958605377 scopus 로고    scopus 로고
    • Clustering metagenomic sequences with interpolated Markov models
    • Kelley, D.R. and Salzberg, S.L. (2010) Clustering metagenomic sequences with interpolated Markov models. BMC Bioinformatics, 11, 544.
    • (2010) BMC Bioinformatics , vol.11 , pp. 544
    • Kelley, D.R.1    Salzberg, S.L.2
  • 20
    • 77955908608 scopus 로고    scopus 로고
    • Sparse nonnegative matrix factorization for clustering
    • Georgia Institute of Technology, Atlanta, Georgia, USA
    • Kim, J. and Park, H. (2008) Sparse nonnegative matrix factorization for clustering. Technical Report GT-CSE-08-01, Georgia Institute of Technology, Atlanta, Georgia, USA.
    • (2008) Technical Report GT-CSE-08-01
    • Kim, J.1    Park, H.2
  • 22
    • 0033592606 scopus 로고    scopus 로고
    • Learning the parts of objects by nonnegative matrix factorization
    • Lee, D.D. and Seung, H.S. (1999) Learning the parts of objects by nonnegative matrix factorization. Nature, 401, 788-791.
    • (1999) Nature , vol.401 , pp. 788-791
    • Lee, D.D.1    Seung, H.S.2
  • 23
    • 84901367862 scopus 로고    scopus 로고
    • A new unsupervised binning approach for metagenomic sequences based on n-grams and automatic feature weighting
    • Liao, R. et al. (2014) A new unsupervised binning approach for metagenomic sequences based on n-grams and automatic feature weighting. IEEE/ACM Trans. Comput. Biol. Bioinform., 11, 42-54.
    • (2014) IEEE/ACM Trans. Comput. Biol. Bioinform. , vol.11 , pp. 42-54
    • Liao, R.1
  • 24
    • 84890434201 scopus 로고    scopus 로고
    • Understanding and enhancement of internal clustering validation measures
    • Liu, Y. et al. (2013) Understanding and enhancement of internal clustering validation measures. IEEE Trans. Cybern., 43, 982-994.
    • (2013) IEEE Trans. Cybern. , vol.43 , pp. 982-994
    • Liu, Y.1
  • 25
    • 84870020971 scopus 로고    scopus 로고
    • Classification of metagenomic sequences: Methods and challenges
    • Mande, S.S. et al. (2012) Classification of metagenomic sequences: methods and challenges. Brief. Bioinform., 13, 669-681.
    • (2012) Brief. Bioinform. , vol.13 , pp. 669-681
    • Mande, S.S.1
  • 26
    • 33845957530 scopus 로고    scopus 로고
    • Accurate phylogenetic classification of variable-length DNA fragments
    • McHardy, A.C. et al. (2007) Accurate phylogenetic classification of variable-length DNA fragments. Nat. Methods, 4, 63-72.
    • (2007) Nat. Methods , vol.4 , pp. 63-72
    • McHardy, A.C.1
  • 27
    • 78650538995 scopus 로고    scopus 로고
    • SPHINXan algorithm for taxonomic binning of metagenomic sequences
    • Mohammed, M.H. et al. (2011) SPHINXan algorithm for taxonomic binning of metagenomic sequences. Bioinformatics, 27, 22-30.
    • (2011) Bioinformatics , vol.27 , pp. 22-30
    • Mohammed, M.H.1
  • 28
    • 84905730761 scopus 로고    scopus 로고
    • Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
    • Nielsen, H.B. et al. (2014) Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat. Biotechnol., 32, 822-828.
    • (2014) Nat. Biotechnol , vol.32 , pp. 822-828
    • Nielsen, H.B.1
  • 29
    • 84870268389 scopus 로고    scopus 로고
    • Analysis of a data matrix and a graph: Metagenomic data and the phylogenetic tree
    • Purdom, E. (2011) Analysis of a data matrix and a graph: metagenomic data and the phylogenetic tree. Ann. Appl. Stat., 2326-2358.
    • (2011) Ann. Appl. Stat. , pp. 2326-2358
    • Purdom, E.1
  • 30
    • 77950251400 scopus 로고    scopus 로고
    • A human gut microbial gene catalogue established by metagenomic sequencing
    • Qin, J. et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464, 59-65.
    • (2010) Nature , vol.464 , pp. 59-65
    • Qin, J.1
  • 31
    • 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
  • 32
    • 78650549608 scopus 로고    scopus 로고
    • NBC: The naive bayes classification tool webserver for taxonomic classification of metagenomic reads
    • Rosen, G.L. et al. (2011) NBC: the naive bayes classification tool webserver for taxonomic classification of metagenomic reads. Bioinformatics, 27, 127-129.
    • (2011) Bioinformatics , vol.27 , pp. 127-129
    • Rosen, G.L.1
  • 33
    • 16244377091 scopus 로고    scopus 로고
    • Determining the number of clusters/segments in hierarchical clustering/segmentation algorithms
    • Boca Raton, Florida, USA
    • Salvador, S. and Chan, P. (2004). Determining the number of clusters/segments in hierarchical clustering/segmentation algorithms. In: Proceedings of the 16th IEEEE International Conference on Tools with AI (ICTAI), Boca Raton, Florida, USA, pp. 576-584.
    • (2004) Proceedings of the 16th IEEEE International Conference on Tools with AI (ICTAI) , pp. 576-584
    • Salvador, S.1    Chan, P.2
  • 34
    • 84871956840 scopus 로고    scopus 로고
    • Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
    • Sharon, I. et al. (2013) Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res., 23, 111-120.
    • (2013) Genome Res. , vol.23 , pp. 111-120
    • Sharon, I.1
  • 35
    • 84863023598 scopus 로고    scopus 로고
    • The impact of Normalization and phylogenetic information on estimating the distance for metagenomes
    • Su, C.H. et al. (2012) The impact of normalization and phylogenetic information on estimating the distance for metagenomes. IEEE/ACM Trans. Comput. Biol. Bioinform., 9, 619-628.
    • (2012) IEEE/ACM Trans. Comput. Biol. Bioinform. , vol.9 , pp. 619-628
    • Su, C.H.1
  • 36
    • 23944492918 scopus 로고    scopus 로고
    • Improved validation index for fuzzy clustering
    • Tang, Y. et al. (2005). Improved validation index for fuzzy clustering. In: American Control Conference, pp. 1120-1125.
    • (2005) American Control Conference , pp. 1120-1125
    • Tang, Y.1
  • 37
    • 27544435126 scopus 로고    scopus 로고
    • Fast protein classification with multiple networks
    • Tsuda, K. et al. (2005) Fast protein classification with multiple networks. Bioinformatics, 21, ii59-ii65.
    • (2005) Bioinformatics , vol.21 , pp. ii59-ii65
    • Tsuda, K.1
  • 38
    • 78349292948 scopus 로고    scopus 로고
    • Alignment-free sequence comparison (II): Theoretical power of comparison statistics
    • Wan, L. et al. (2010) Alignment-free sequence comparison (ii): theoretical power of comparison statistics. J. Comput. Biol., 17, 1467-1490.
    • (2010) J. Comput. Biol. , vol.17 , pp. 1467-1490
    • Wan, L.1
  • 39
    • 84946487753 scopus 로고    scopus 로고
    • Comparing the performance of biomedical clustering methods
    • page (epub ahead of print)
    • Wiwie, C. et al. (2015) Comparing the performance of biomedical clustering methods. Nat. Methods, page (epub ahead of print).
    • (2015) Nat. Methods
    • Wiwie, C.1
  • 40
    • 84899090573 scopus 로고    scopus 로고
    • Kraken: Ultrafast metagenomic sequence classification using exact alignments
    • Wood, D.E. and Salzberg, S.L. (2014) Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol., 15, R46.
    • (2014) Genome Biol. , vol.15 , pp. R46
    • Wood, D.E.1    Salzberg, S.L.2
  • 41
    • 79952425617 scopus 로고    scopus 로고
    • A novel abundance-based algorithm for binning metagenomic sequences using l-tuples
    • Wu, Y.W. and Ye, Y. (2011) A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. J. Comput. Biol., 18, 523-534.
    • (2011) J. Comput. Biol. , vol.18 , pp. 523-534
    • Wu, Y.W.1    Ye, Y.2
  • 42
    • 84957911451 scopus 로고    scopus 로고
    • MaxBin 2.0: An automated binning algorithm to recover genomes from multiple metagenomic datasets
    • Wu, Y.W. et al. (2016) MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics, 32, 605-607.
    • (2016) Bioinformatics , vol.32 , pp. 605-607
    • Wu, Y.W.1
  • 43
    • 77952894198 scopus 로고    scopus 로고
    • Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers
    • Yang, B. et al. (2010) Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers. BMC Bioinformatics, 11, S5.
    • (2010) BMC Bioinformatics , vol.11 , pp. S5
    • Yang, B.1
  • 44
    • 67149088568 scopus 로고    scopus 로고
    • An ORFome assembly approach to metagenomics sequences analysis
    • Ye, Y. and Tang, H. (2009) An ORFome assembly approach to metagenomics sequences analysis. J. Bioinform. Comput. Biol., 7, 455-471.
    • (2009) J. Bioinform. Comput. Biol. , vol.7 , pp. 455-471
    • Ye, Y.1    Tang, H.2


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