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Enhancing genome recovery across metagenomic samples using MAGmax.

Arangasamy Yazhini·Johannes Söding
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Abstract

SUMMARY: The number of metagenome-assembled genomes (MAGs) is rapidly increasing with the growing scale of metagenomic studies, driving fast progress in microbiome research. Sample-wise assembly has become the standard due to its computational efficiency and strain-level resolution. It requires dereplication, the removal of near-identical genomes assembled in different metagenomic samples. We present MAGmax, an efficient dereplication tool that enhances both the quantity and quality of MAGs through a strategy of bin merging and reassembly. Unlike dRep, which selects a single representative bin per genome cluster, MAGmax merges multiple bins within a cluster and reassembles them to increase coverage. MAGmax produces more dereplicated, higher-quality MAGs than dRep at 1.6× its speed and using three times less memory. AVAILABILITY AND IMPLEMENTATION: The MAGmax open source software, implemented in Rust, is available under the GPLv3 license at https://github.com/soedinglab/MAGmax.

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MetagenomicsSoftwareMetagenomeAlgorithmsJournal ArticleResearch Support, Non-U.S. Gov't

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Arangasamy Yazhini, Johannes Söding. 2025-10-02. Enhancing genome recovery across metagenomic samples using MAGmax.. https://doi.org/10.1093/bioinformatics%2Fbtaf538

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