Definition
Binning is unsupervised clustering of metagenomic sequences into an unknown set of species.
AbundanceBin is a binning tool utilizing the different abundances of the species in a community.
Introduction
Binning is one of the challenging problems in the metagenomics field. It has two main applications. One application is for studying the structure of microbial communities. The other application is for improving the downstream analysis of metagenomic sequences, including metagenome assembly (which has shown to be extremely difficult), considering that assembling reads one bin at a time significantly reduces the complexity of the metagenome assembly problem.
Composition-based methods have been the main approaches to unsupervised classification of reads. The basis of these approaches is that the genome composition (G + C content, dinucleotide frequencies, and synonymous codon usage) vary among organisms and are generally characteristic of evolutionary lineages. Tools in this...
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References
Baran Y, Halperin E. Joint analysis of multiple metagenomic samples. PLoS Comput Biol. 2012;8(2):e1002373.
Cole JR, Wang Q, Cardenas E, et al. The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009;37(Database issue):D141–5.
Diaz NN, Krause L, Goesmann A, et al. TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics. 2009;10:56.
Gori F, Folino G, Jetten MS, et al. MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks. Bioinformatics. 2011;27(2):196–203.
Huson DH, Mitra S. Introduction to the analysis of environmental sequences: metagenomics with MEGAN. Methods Mol Biol. 2012;856:415–29.
Huson DH, Auch AF, Qi J, et al. MEGAN analysis of metagenomic data. Genome Res. 2007;17(3):377–86.
Krause L, Diaz NN, Goesmann A, et al. Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res. 2008;36(7):2230–9.
Leung HC, Yiu SM, Yang B, et al. A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio. Bioinformatics. 2011;27(11):1489–95.
Liu B, Gibbons T, Ghodsi M, et al. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics. 2011;12 Suppl 2:S4.
Rosen GL, Reichenberger ER, Rosenfeld AM. NBC: the naive bayes classification tool webserver for taxonomic classification of metagenomic reads. Bioinformatics. 2011;27(1):127–9.
Stark M, Berger SA, Stamatakis A, et al. MLTreeMap–accurate maximum likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies. BMC Genomics. 2010;11:461.
Teeling H, Waldmann J, Lombardot T, et al. TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. BMC Bioinformatics. 2004;5:163.
Wang Y, Leung HC, Yiu SM, et al. MetaCluster 4.0: a novel binning algorithm for NGS reads and huge number of species. J Comput Biol. 2012;19(2):241–9.
Wu YW, Ye Y. A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. J Comput Biol. 2011;18(3):523–34.
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Ye, Y. (2015). AbundanceBin, Metagenomic Sequencing. In: Nelson, K.E. (eds) Encyclopedia of Metagenomics. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-7478-5_29
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DOI: https://doi.org/10.1007/978-1-4899-7478-5_29
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Publisher Name: Springer, Boston, MA
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Online ISBN: 978-1-4899-7478-5
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