A comprehensive assessment of tandem repeat genotyping methods for Nanopore long-read genomes
No single genotyper emerged as consistently best across all assessments, but strong contenders emerged in each. Our results demonstrate that length accuracy (a typical benchmarking approach) alone overestimates TR genotyping performance. Sequence-level benchmarking is essential for selecting tools best-suited for population studies and clinical diagnostics. This work provides practical guidance for tool selection and highlights key priorities for future long-read TR genotyping method development.
Authors
- Bida Gu (ORCID: https://orcid.org/0000-0001-8575-997X)
- Elbay Aliyev (ORCID: https://orcid.org/0000-0002-6469-1854)
- Denis M. Nyaga (ORCID: https://orcid.org/0000-0001-6240-4017)
- Elizabeth A. Ostrowski (ORCID: https://orcid.org/0000-0002-9784-5979)
- Akshay Kumar Avvaru (ORCID: https://orcid.org/0000-0003-4698-9363)
- Sophia B Gibson (ORCID: https://orcid.org/0000-0001-9839-9045)
- Ben Weisburd
- Wouter De Coster
- Garrison M. Arner
- Danny E. Miller
- Claudia Gonzaga-Jauregui
Institutions
- Broad Institute (US)
- University of Southern California (US)
- University of Antwerp (BE)
- University of Auckland (NZ)
- University of Washington (US)
- University of Washington Medical Center (US)
- VIB-UAntwerp Center for Molecular Neurology (BE)
- Brotman Baty Institute (US)
- University of Washington Bothell (US)
- University of Colorado Anschutz Medical Campus (US)
- Metropolitan State University of Denver (US)
- Universidad Nacional Autónoma de México (MX)
Publication Details
- Journal
- bioRxiv (Cold Spring Harbor Laboratory)
- Published
- 2026-03-03
- DOI
- https://doi.org/10.64898/2026.02.28.708646
- Primary Topic
- Genetic Neurodegenerative Diseases
- Type
- article
- Field-Weighted Citation Impact
- 0.00