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mm2-ivh: simple and precise overlap detection in alpha satellite HORs with interval hashing
Hajime Suzuki1, Masahiro Sugawa1, Yoshitaka Sakamoto1
1Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan.
Bioinformatics (Oxford, England)
|December 3, 2025
Summary
We developed interval hashing to differentiate identical k-mers from various repeat sequences, improving haplotype reconstruction in complex regions like alpha satellite HORs.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Complex repeat arrays, such as alpha satellite higher-order repeats (HORs), pose challenges for sequence assembly due to repetitive elements.
- Distinguishing identical k-mers originating from different repeat instances is crucial for accurate genomic analysis.
Purpose of the Study:
- To introduce a novel algorithm, interval hashing, designed to resolve ambiguities in k-mer identification within complex repeat structures.
- To enhance the accuracy of haplotype reconstruction in repetitive genomic regions.
Main Methods:
- Developed and implemented the interval hashing algorithm as a modification of the minimap2 tool, named mm2-ivh.
- Applied mm2-ivh to the local assembly of alpha satellite HORs.
Main Results:
- Interval hashing successfully distinguishes identical k-mers originating from different repeat sequences.
- The mm2-ivh implementation demonstrated superior performance in reconstructing more haplotypes compared to standard minimizer-based assemblers in alpha satellite HORs.
Conclusions:
- Interval hashing provides a robust solution for analyzing complex repeat arrays.
- mm2-ivh offers improved accuracy for haplotype reconstruction in challenging genomic regions, particularly alpha satellite HORs.
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