TY  - JOUR
A1  - Shivakumar, Vikram S.
A1  - Langmead, Ben
T1  - Partitioned multi-MUM finding for scalable pangenomics with MumemtoM
Y1  - 2026/02/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 397 
EP  - 404 
DO  - 10.1101/gr.280940.125 
VL  - 36 
IS  - 2 
UR  - http://genome.cshlp.org/content/36/2/397.abstract 
N2  - Pangenome collections are growing to hundreds of high-quality genomes. This necessitates scalable methods for constructing pangenome alignments that can incorporate newly sequenced assemblies. We previously developed Mumemto, which computes maximal unique matches (multi-MUMs) across pangenomes using compressed indexing. In this work, we introduce MumemtoM (Mumemto Merge), comprising two new partitioning and merging strategies. Both strategies enable highly parallel, memory-efficient, and updateable computation of multi-MUMs. One of the strategies, called string-based merging, is also capable of conducting the merges in a way that follows the shape of a phylogenetic tree, naturally yielding the multi-MUM for the tree’s internal nodes as well as the root. With these strategies, Mumemto now scales to 474 human haplotypes, the only multi-MUM method able to do so. It also introduces a time–memory tradeoff that allows Mumemto to be tailored to more scenarios, including in resource-limited settings. 
ER  -