Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation
Sign Up to like & getrecommendations! Published in 2018 at "Nature biotechnology"
DOI: 10.1038/nbt.4037
Abstract: Shotgun metagenomics methods enable characterization of microbial communities in human microbiome and environmental samples. Assembly of metagenome sequences does not output whole genomes, so computational binning methods have been developed to cluster sequences into genome… read more here.
Keywords: methylation; binning association; host; metagenomic binning ... See more keywords
Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes
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DOI: 10.1038/s42003-020-0856-x
Abstract: The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome.… read more here.
Keywords: binning enables; metagenomic binning; niche; wide metagenomic ... See more keywords
Metagenomic binning through low-density hashing
Sign Up to like & getrecommendations! Published in 2019 at "Bioinformatics"
DOI: 10.1093/bioinformatics/bty611
Abstract: Motivation: Vastly greater quantities of microbial genome data are being generated where environmental samples mix together the DNA from many different species. Here, we present Opal for metagenomic binning, the task of identifying the origin… read more here.
Keywords: binning low; low density; density hashing; metagenomic binning ... See more keywords
Metagenomic binning with assembly graph embeddings
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DOI: 10.1101/2022.02.25.481923
Abstract: Despite recent advancements in sequencing technologies and assembly methods, obtaining high-quality microbial genomes from metagenomic samples is still not a trivial task. Current metagenomic binners do not take full advantage of assembly graphs and are… read more here.
Keywords: graph; assembly graph; graph embeddings; binning assembly ... See more keywords