PreprintCC BY-NDbioRxiv
Nailpolish: Reference-free UMI deduplication and consensus read generation
- 1The Walter and Eliza Hall Institute of Medical Research
Abstract
Long-read sequencing captures full-length transcripts but suffers elevated error rates, and PCR duplicates can distort quantification unless accounted for with UMIs. We present Nailpolish, a fast reference-free tool that error-corrects and deduplicates UMI-tagged long reads by generating consensus sequences via partial order alignment, while separating false duplicates arising from UMI collisions. Across eleven Oxford Nanopore Technologies and Pacific Biosciences datasets spanning bulk, single-cell, spatial, and targeted protocols, Nailpolish reduced per-read error rates and outperformed existing deduplication tools.
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BibTeX
@misc{cheng2026nailpolish,
title = {{Nailpolish: Reference-free UMI deduplication and consensus read generation}},
author = {O. Y. Cheng and J. W. Tan and N. M. Davidson},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.25.754331},
url = {https://www.biorxiv.org/content/10.64898/2026.09.25.754331v1},
note = {CC BY-ND},
}
RIS
TY - UNPB
TI - Nailpolish: Reference-free UMI deduplication and consensus read generation
AU - O. Y. Cheng
AU - J. W. Tan
AU - N. M. Davidson
PY - 2026
DA - 2026/09/25
PB - bioRxiv
DO - 10.64898/2026.09.25.754331
UR - https://www.biorxiv.org/content/10.64898/2026.09.25.754331v1
AB - Long-read sequencing captures full-length transcripts but suffers elevated error rates, and PCR duplicates can distort quantification unless accounted for with UMIs. We present Nailpolish, a fast reference-free tool that error-corrects and deduplicates UMI-tagged long reads by generating consensus sequences via partial order alignment, while separating false duplicates arising from UMI collisions. Across eleven Oxford Nanopore Technologies and Pacific Biosciences datasets spanning bulk, single-cell, spatial, and targeted protocols, Nailpolish reduced per-read error rates and outperformed existing deduplication tools.
ER -