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Updated: Sep 19, 2025

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Mumemto: efficient maximal matching across pangenomes.

Vikram S Shivakumar1, Ben Langmead2

  • 1Department of Computer Science, Johns Hopkins University, Baltimore, USA. vshivak1@jhu.edu.

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|June 17, 2025
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Summary

Mumemto efficiently computes multi-sequence maximal unique matches (multi-MUMs) for large pangenome construction. This tool aids in genome alignment, structural variation analysis, and assembly validation, accelerating comparative genomics research.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Pangenome construction requires aligning genomes to common coordinates, a computationally intensive process.
  • Multi-sequence maximal unique matches (multi-MUMs) are crucial for framing and solving multiple sequence alignment problems in pangenomics.

Purpose of the Study:

  • To introduce Mumemto, a novel computational tool designed for efficient multi-MUM computation across large pangenomes.
  • To enable visualization of synteny, identification of aberrant genome assemblies, and analysis of pangenome conservation and structural variations.

Main Methods:

  • Mumemto computes multi-MUMs and other match types using C++ and Python.
  • The tool was benchmarked on large datasets, including 320 human assemblies (960GB) and hundreds of fungal assemblies.

Main Results:

  • Mumemto processed 320 human assemblies in 25.7 hours using 800 GB of memory.
  • The tool achieved rapid analysis of hundreds of fungal assemblies in minutes.
  • Mumemto facilitates visualization of genomic synteny and identification of structural variations.

Conclusions:

  • Mumemto offers a computationally efficient solution for multi-MUM identification in large-scale pangenomics.
  • The tool enhances the analysis of genome assemblies, structural variations, and pangenome conservation.
  • Mumemto is available as open-source software, promoting accessibility and further development in comparative genomics.