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

## TL;DR

This paper introduces mm2-ivh, a new algorithm that improves the detection of overlapping DNA repeats, especially in alpha satellite HORs.

## Contribution

The novel contribution is the interval hashing algorithm, which enhances haplotype reconstruction in complex repeat regions.

## Key findings

- mm2-ivh outperforms standard assemblers in reconstructing haplotypes from alpha satellite HORs.
- Interval hashing distinguishes k-mers from different repeat sequences more accurately.

## Abstract

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.

mm2-ivh is available under the MIT license at https://github.com/ocxtal/mm2-ivh and runs on common Unix-compatible systems.