Reference : binny: an automated binning algorithm to recover high-quality genomes from complex me...
Scientific journals : Article
Life sciences : Genetics & genetic processes
Physical, chemical, mathematical & earth Sciences : Multidisciplinary, general & others
Systems Biomedicine
http://hdl.handle.net/10993/52754
binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets
English
Hickl, Oskar mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core]
Queirós, Pedro [> >]
Wilmes, Paul mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology]
May, Patrick mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core]
Heintz-Buschart, Anna [> >]
13-Oct-2022
Briefings in Bioinformatics
Yes
International
1477-4054
[en] metagenome-assembled genome ; marker gene sets ; iterative clustering ; embedding ; dimensionality reduction ; t-SNE ; MAGs
[en] The reconstruction of genomes is a critical step in genome-resolved metagenomics and for multi-omic data integration from microbial communities. Here, we present binny, a binning tool that produces high-quality metagenome-assembled genomes (MAG) from both contiguous and highly fragmented genomes. Based on established metrics, binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods and finds unique genomes that could not be detected by other methods. binny uses k-mer-composition and coverage by metagenomic reads for iterative, nonlinear dimension reduction of genomic signatures as well as subsequent automated contig clustering with cluster assessment using lineage-specific marker gene sets. When compared with seven widely used binning algorithms, binny provides substantial amounts of uniquely identified MAGs and almost always recovers the most near-complete (⁠>95% pure, >90% complete) and high-quality (⁠>90% pure, >70% complete) genomes from simulated datasets from the Critical Assessment of Metagenome Interpretation initiative, as well as substantially more high-quality draft genomes, as defined by the Minimum Information about a Metagenome-Assembled Genome standard, from a real-world benchmark comprised of metagenomes from various environments than any other tested method.
Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) ; Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group)
Fonds National de la Recherche - FnR
http://hdl.handle.net/10993/52754
10.1093/bib/bbac431
https://doi.org/10.1093/bib/bbac431
FnR ; FNR11823097 > Paul Wilmes > MICROH-DTU > Microbiomes In One Health > 01/09/2018 > 28/02/2025 > 2017

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