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<p>Aligning genomes into common coordinates is central to pangenome construction, though computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) help 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 assemblies (960GB) in 25.7 h with 800 GB of memory and hundreds of fungal assemblies in minutes. Mumemto is implemented in C++ and Python and available open-source at <a href="https://github.com/vikshiv/mumemto">https://github.com/vikshiv/mumemto</a> (v1.1.1 at <ExternalRef> <RefSource>doi.org/10.5281/zenodo.15053447</RefSource> <RefTarget Address="doi.org/10.5281/zenodo.15053447" TargetType="Other" /> </ExternalRef>).</p>

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Mumemto: efficient maximal matching across pangenomes

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年6月17日

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  • Vikram S. Shivakumar,
  • Ben Langmead

摘要

Aligning genomes into common coordinates is central to pangenome construction, though computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) help 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 assemblies (960GB) in 25.7 h with 800 GB of memory and hundreds of fungal assemblies in minutes. Mumemto is implemented in C++ and Python and available open-source at https://github.com/vikshiv/mumemto (v1.1.1 at doi.org/10.5281/zenodo.15053447 ).