mm2-ivh: simple and precise overlap detection in alpha satellite HORs with interval hashing.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 41335462.
- Also identified by DOI 10.1093/bioinformatics/btaf648 and PMC identifier 12766915.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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.
Medical subject headings
- Algorithms
- Software
- DNA, Satellite
- Sequence Analysis, DNA