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bioRxiv · 10.1101/2025.07.11.664273

mm2-ivh: simple and precise overlap detection in alpha satellite HORs with interval hashing

Suzuki, H.·Sugawa, M.·Sakamoto, Y.·Shiraishi, Y.
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Abstract

SummaryWe propose a new algorithm, "interval hashing," which distinguishes identical k-mers arising from different repeat sequences, particularly in complex repeat arrays such as alpha satellite HORs. We implement this algorithm as a fork of minimap2, named mm2-ivh. In local assembly of alpha satellite HORs, mm2-ivh accurately reconstructs more haplotypes than assemblers using standard minimizers. Availabilitymm2-ivh is available under the MIT license at https://github.com/ocxtal/mm2-ivh and runs on common Unix-compatible systems.

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Suzuki, H., Sugawa, M., Sakamoto, Y., Shiraishi, Y.. 2025-07-17. mm2-ivh: simple and precise overlap detection in alpha satellite HORs with interval hashing. https://doi.org/10.1101/2025.07.11.664273

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