iiinova — where your digital self keeps evolving

Reposted by Stephen Hwang

Vikram Shivakumar @vikramshivakumar.bsky.social · 26/02/2025

We ran Mumemto on 474 human assemblies from @humanpangenome.bsky.social to find syntenic regions using MUMs. Mumemto scales remarkably well to large pangenomes thanks to compressed-space algos! It took under 2 days across 7 nodes (each using ~500 GB memory).

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Reposted by Stephen Hwang

Vikram Shivakumar @vikramshivakumar.bsky.social · 06/01/2025

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.

biorxiv.org

Mumemto: efficient maximal matching across pangenomes

Aligning genomes into common coordinates is central to pangenome analysis and construction, but it is also computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) are guideposts ...

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Reposted by Stephen Hwang

Ben Langmead @benlangmead.bsky.social · 11/12/2024

Very excited to see Movi (by @mohsenzakeri.bsky.social) now out in iScience: www.cell.com/iscience/ful.... Movi builds on the "move structure" pangenome index, a compressed full-text index and close cousin to r-index. Compared to r-index, the move structure is simpler and more cache-efficient.

cell.com

Movi: A fast and cache-efficient full-text pangenome index

Biocomputational method; Classification of bioinformatical subject; Genomic analysis

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Reposted by Stephen Hwang

Mohsen Zakeri @mohsenzakeri.bsky.social · 07/11/2023

1/5 We (Nate Brown, @oahmed.bsky.social, Travis Gagie, and @benlangmead.bsky.social) developed Movi, a cache-efficient full-text pangenome index. It's the fastest full-text index for pangenomes, particularly appropriate for adaptive sampling where time budget is important.

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