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bioRxiv · 10.1101/2025.01.05.631388

Mumemto: efficient maximal matching across pangenomes

Shivakumar, V. S.·Langmead, B.
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Abstract

Aligning genomes into common coordinates is central to pangenome analysis and construction, but it is also computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) are guideposts for core genome alignments, helping to frame and solve the multiple alignment problem. We introduce Mumemto, a tool that computes multi-MUMs and other match types across large pangenomes. Mumemto allows for visualization of synteny, reveals aberrant assemblies and scaffolds, and highlights pangenome conservation and structural variation. Mumemto computes multi-MUMs across 320 human genome assemblies (960GB) in 25.7 hours with under 800 GB of memory, and over hundreds of fungal genome assemblies in minutes. Mumemto is implemented in C++ and Python and available open-source at https://github.com/vikshiv/mumemto.

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Shivakumar, V. S., Langmead, B.. 2025-01-05. Mumemto: efficient maximal matching across pangenomes. https://doi.org/10.1101/2025.01.05.631388

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