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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Ye, Y. (2013). AbundanceBin, Metagenomic Sequencing. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_29-4
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DOI: https://doi.org/10.1007/978-1-4614-6418-1_29-4
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Publisher Name: Springer, New York, NY
Online ISBN: 978-1-4614-6418-1
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