ArticlemSystems2022
MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics.
Article in mSystems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 19 citations in OpenAlex.
- metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.Gut microbes · 2026Article
- Community-driven updates for comprehensive long-read metagenomics and enhanced binning in nf-core/mag v5.Bioinformatics (Oxford, England) · 2026Article
- MeioBIOME: A snakemake workflow for the parallel analysis of meiofaunal genomes and host-associated bacteria/archaea.bioRxiv : the preprint server for biology · 2026Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.Nucleic acids research · 2025Article
- Highly-accurate prediction of colorectal cancer through low abundance uncultivated genomes recovered using metagenomic co-assembly and binning approach.BMC cancer · 2025Article
- Genome-resolved metagenomics: a game changer for microbiome medicine.Experimental & molecular medicine · 2024Review
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing.Microbial biotechnology · 2024Review
- The association between the composition of the early-life intestinal microbiome and eczema in the first year of life.Frontiers in microbiomes · 2023Article
- Metaphor-A workflow for streamlined assembly and binning of metagenomes.GigaScience · 2022Article
- Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros.PLoS biology · 2022Article
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Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenome-assembled genomes (MAGs) represent individual genomes recovered from metagenomic data. MAGs are extremely useful to analyze uncultured microbial genomic diversity, as well as to characterize associated functional and metabolic potential in natural environments. Recent computational developments have considerably improved MAG reconstruction but also emphasized several limitations, such as the nonbinning of sequence regions with repetitions or distinct nucleotidic composition. Different assembly and binning strategies are often used; however, it still remains unclear which assembly strategy, in combination with which binning approach, offers the best performance for MAG recovery. Several workflows have been proposed in order to reconstruct MAGs, but users are usually limited to single-metagenome assembly or need to manually define sets of metagenomes to coassemble prior to genome binning. Here, we present MAGNETO, an automated workflow dedicated to MAG reconstruction, which includes a fully-automated coassembly step informed by optimal clustering of metagenomic distances, and implements complementary genome binning strategies, for improving MAG recovery. MAGNETO is implemented as a Snakemake workflow and is available at: https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto.
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