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bioRxiv · 10.1101/2025.05.28.656617

Enhancing genome recovery across metagenomic samples using MAGmax

Arangasamy, Y.·Soeding, J.
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Abstract

SummaryThe 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 re-assembly. 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 1.6x its speed and using three times less memory. Availability and implementationThe MAGmax open source software, implemented in Rust, is available under the GPLv3 license at https://github.com/soedinglab/MAGmax.

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Arangasamy, Y., Soeding, J.. 2025-06-01. Enhancing genome recovery across metagenomic samples using MAGmax. https://doi.org/10.1101/2025.05.28.656617

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