Enhancing genome recovery across metagenomic samples using MAGmax.

IF 5.4

Bioinformatics (Oxford, England) Pub Date : 2025-09-26 DOI:10.1093/bioinformatics/btaf538

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.

Supplementary information: Supplementary data are available at Bioinformatics online.

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利用MAGmax增强宏基因组样本的基因组恢复。

摘要：随着宏基因组研究规模的扩大，宏基因组组装基因组（MAGs）的数量迅速增加，推动了微生物组研究的快速发展。基于样本的装配由于其计算效率和应变级分辨率而成为标准。它需要去复制，去除在不同宏基因组样本中组装的几乎相同的基因组。我们提出了MAGmax，一个有效的反复制工具，通过bin合并和重组策略提高了MAGs的数量和质量。与dRep不同的是，它在每个基因组簇中选择一个具有代表性的bin， MAGmax在一个簇中合并多个bin并重新组装它们以增加覆盖率。MAGmax的速度是dRep的1.6倍，使用的内存却只有dRep的三分之一。可用性和实现：MAGmax开源软件，用Rust实现，在GPLv3许可下可在https://github.com/soedinglab/MAGmax.Supplementary上获得信息：补充数据可在Bioinformatics在线获得。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Bioinformatics (Oxford, England)

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