Mumemto: efficient maximal matching across pangenomes

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-06-17 DOI:10.1186/s13059-025-03644-0

Vikram S. Shivakumar, Ben Langmead

引用次数: 0

Abstract

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 ).

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Mumemto：跨泛基因组的高效最大匹配

将基因组对齐到共同坐标是泛基因组构建的核心，尽管计算成本很高。多序列最大唯一匹配（multi- mum）有助于构建和解决多重对齐问题。我们介绍Mumemto，一个计算跨大泛基因组的多mum和其他匹配类型的工具。Mumemto允许对合成进行可视化，揭示异常的组装和支架，并突出泛基因组的保护和结构变化。Mumemto在25.7小时内计算320个人类组装（960GB）的多mum， 800 GB内存和数百个真菌组装在几分钟内。Mumemto是用c++和Python实现的，可以在https://github.com/vikshiv/mumemto上获得开源（v1.1.1在doi.org/10.5281/zenodo.15053447上）。

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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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

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