ArticleGenome biology2025
Mumemto: efficient maximal matching across pangenomes.
Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Navigating the pangenome coordinate system with Shredtools.bioRxiv : the preprint server for biology · 2026Article
- Building genomic data structures from compressed representations using prefix-free parsing.Genome research · 2026Review
- Min-frame transformation enables more sensitive viral genome alignment.bioRxiv : the preprint server for biology · 2026Article
- Partitioned multi-MUM finding for scalable pangenomics with MumemtoM.Genome research · 2026Article
- Col-BWT: Pangenomic Seed Chaining with Maximal Matches Improves Read Classification.Journal of computational biology : a journal of computational molecular cell biology · 2026Article
- Prefix-free parsing for merging big BWTs.International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium) · 2026Article
- Bounding the Average Move Structure Query for Faster and Smaller RLBWT Permutations.LIPIcs : Leibniz international proceedings in informatics · 2026Article
- PG-SCUnK: measuring pangenome graph representativeness using single-copy and universal K-mers.BMC bioinformatics · 2025Article
- Partitioned Multi-MUM finding for scalable pangenomics.bioRxiv : the preprint server for biology · 2025Article
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2 authors.
Funding
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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.