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bioRxiv · 10.64898/2026.07.03.736354

Navigating the pangenome coordinate system with Shredtools

Shivakumar, V. S.·Langmead, B.
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Abstract

Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and represent conserved stretches of columns in the underlying MSA. We introduce Shredtools, which uses multi-MUMs as pangenome waypoints and allows for sophisticated queries in pangenome coordinates. Its primary query is extract, which takes an interval of one sequence and extracts the smallest window containing it that is syntenic pangenome-wide. Shredtools extract query can extract a gene region from 476 human genomes in half a second. Other queries help to refine these results, by finding local exact matches to improve the density of multi-MUM coverage ("enhance") and by selectively discarding sequences to improve the precision of the syntenic region ("zoom"). The Shredtools web interface (available at https://vikshiv.github.io/shredtools) allows for client-side handling of extract queries with index queries handled via simple and fast HTTP Range requests, simplifying usage and enabling pangenomescale discoveries.

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Shivakumar, V. S., Langmead, B.. 2026-07-08. Navigating the pangenome coordinate system with Shredtools. https://doi.org/10.64898/2026.07.03.736354

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