Enhancing genome recovery across metagenomic samples using MAGmax

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.

Figure 1.

(a) Overview of MAGmax. The blue star marks a high-quality bin. (b) Complementary cumulative distribution of the number of dereplicated genomic bins over the bin quality score (completeness − 5 $\times$ purity) in combination with three popular binners. (c) Quality scores of dRep bins (y-axis) and the corresponding MAGmax bins (x-axis) based on genomic cluster membership. Grey/blue circles: MAGmax and dRep bins are identical/different. (d) Scatter plot showing quality scores of merged and reassembled bins (x-axis) versus input bins (y-axis). Blue circles represent the highest-quality bins within each genomic cluster, while cyan circles indicate the other input bins. Vertical lines connect the input bins that were used for merging and reassembly. (e) Runtime (in minutes) and peak memory usage (in GB).