Excited to share a preprint for (w/ @benlangmead.bsky.social) our new tool, Mumemto, on biorxiv! Mumemto finds multi-MUMs across pangenomes (i.e. mummer but for pangenomes). It can rapidly visualize synteny, identify misassemblies, and accelerate core genome and multiple alignment, highlighting SVs. - ThreadSky

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vikramshivakumar.bsky.social • 51 days ago

Excited to share a preprint for (w/ @benlangmead.bsky.social) our new tool, Mumemto, on https://www.biorxiv.org/content/10.1101/2025.01.05.631388v1! Mumemto finds multi-MUMs across pangenomes (i.e. mummer but for pangenomes). It can rapidly visualize synteny, identify misassemblies, and accelerate core genome and multiple alignment, highlighting SVs.

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vikramshivakumar.bsky.social•51 days ago

Mumemto uses prefix-free parsing, a compressed-space method to compute the enhance suffix array, to efficiently index large pangenome collections. This makes it quick and memory efficient, with remarkable scaling, enabling multi-MUM computation across hundreds of HPRC assemblies.

vikramshivakumar.bsky.social•51 days ago

Mumemto can visualize multi-MUM synteny to reveal large-scale pangenome structure. We also showed that multi-MUMs can reveal potential misassemblies (e.g one reported in HPRC v1) and scaffolding errors (contigs are oriented to match a reference w/o the pangenome context revealing a common inversion)

vikramshivakumar.bsky.social•51 days ago

We think Mumemto is an essential first-step for pangenome QC and visualization when sequencing new pangenome assembly collections (especially complete and T2T!). Software is here: https://github.com/vikshiv/mumemto

vikramshivakumar.bsky.social•51 days ago

p.s. Mumemto is already being used to improve read classification with the r-index (https://www.biorxiv.org/content/10.1101/2024.10.29.620953v1), some great work by Nate Brown.

vikramshivakumar.bsky.social•51 days ago

p.p.s here's a logo I designed for Mumemto (pronounced like memento) inspired by the film.

benlangmead.bsky.social•51 days ago

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