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CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. AlthoughExpand
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An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate.Expand
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STAMP: statistical analysis of taxonomic and functional profiles
UNLABELLED STAMP is a graphical software package that provides statistical hypothesis tests and exploratory plots for analysing taxonomic and functional profiles. It supports tests for comparingExpand
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Community structure and metabolism through reconstruction of microbial genomes from the environment
Microbial communities are vital in the functioning of all ecosystems; however, most microorganisms are uncultivated, and their roles in natural systems are unclear. Here, using random shotgunExpand
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Insights into the phylogeny and coding potential of microbial dark matter
Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes thatExpand
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Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
SUMMARY Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNAExpand
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Defining the core Arabidopsis thaliana root microbiome
Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root)Expand
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A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability toExpand
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Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
Reference genomes are required to understand the diverse roles of microorganisms in ecology, evolution, human and animal health, but most species remain uncultured. Here we present a sequenceExpand
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Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage
Anaerobic oxidation of methane (AOM) is critical for controlling the flux of methane from anoxic environments. AOM coupled to iron, manganese and sulphate reduction have been demonstrated inExpand
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