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July 17th, 2025
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National Cancer Center Research Institute
bioinformatics
biorxiv

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

Suzuki, H.Open in Google Scholar•Sugawa, M.Open in Google Scholar•Sakamoto, Y.Open in Google Scholar•Shiraishi, Y.Open in Google Scholar

Summary: We 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. Availability: mm2-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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