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binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets 2021.12.22.473795
Hickl, Oskar; Teixeira Queiros, Pedro; Wilmes, Paul et al.
2021
 

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Keywords :
binning; metagenomic reconstructed genomes; metagenomics
Abstract :
[en] The reconstruction of genomes is a critical step in genome-resolved metagenomics as well as for multi-omic data integration from microbial communities. Here, we present binny, a binning tool that produces high-quality metagenome-assembled genomes from both contiguous and highly fragmented genomes. Based on established metrics, binny outperforms existing 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, non-linear dimension reduction of genomic signatures as well as subsequent automated contig clustering with cluster assessment using lineage-specific marker gene sets.When compared to five widely used binning algorithms, binny recovers the most near-complete (\>95 pure, \>90 complete) and high-quality (\>90 pure, \>70 complete) genomes from simulated data sets from the Critical Assessment of Metagenome Interpretation (CAMI) initiative, as well as from a real-world benchmark comprised of metagenomes from various environments. binny is implemented as Snakemake workflow and available from https://github.com/a-h-b/binny.Competing Interest StatementThe authors have declared no competing interest.
Research center :
- Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group)
- Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group)
Disciplines :
Genetics & genetic processes
Environmental sciences & ecology
Author, co-author :
Hickl, Oskar ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core
Teixeira Queiros, Pedro ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology
Wilmes, Paul ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology
May, Patrick  ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core
Heintz-Buschart, Anna
Language :
English
Title :
binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets 2021.12.22.473795
Publication date :
23 December 2021
Publisher :
Cold Spring Harbor Laboratory
Focus Area :
Systems Biomedicine
FnR Project :
FNR11823097 - Microbiomes In One Health, 2017 (01/09/2018-28/02/2025) - Paul Wilmes
Funders :
FNR - Fonds National de la Recherche [LU]
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since 24 January 2022

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