QuickSeg: A fast, versatile and accurate algorithm for genomic copy number segmentation using dynamic programming
- 1University of Copenhagen
Abstract
Copy number alterations are among the most common genomic aberrations in cancer and their accurate identification relies on robust segmentation of sequencing read-depth signals. Existing segmentation methods typically balance computational efficiency against segmentation accuracy and remain sensitive to technical artifacts present in sequencing data. Here, we present QuickSeg, a fast and versatile methodology that uses an exact dynamic programming algorithm to detect copy number segments using median-based error function. Motivated by the observation that sequencing depth distributions contain a small but pervasive population of outlying observations, this approach provides increased robustness to technical noise while simultaneously reducing the computational complexity of the segmentation problem. Across whole-genome sequencing of cancer cohorts, using breakpoint-supported somatic copy number alterations, we demonstrate improved segmentation precision over two widely used baseline methods, Circular Binary Segmentation (CBS) and Piecewise Constant Fitting (PCF), across a broad range of sensitivity thresholds. QuickSeg also consistently outperformed both methods with respect to runtime and memory usage. Collectively, our results show that robust median-based optimization provides both biological and computational advantages for copy number segmentation, enabling accurate analysis of large sequencing cohorts with minimal computational requirements.
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BibTeX
@misc{schlotmann2026quickseg,
title = {{QuickSeg: A fast, versatile and accurate algorithm for genomic copy number segmentation using dynamic programming}},
author = {B. Schlotmann and F. Favero and A. Locallo and J. L. Weischenfeldt},
howpublished = {bioRxiv},
year = {2026},
month = aug,
doi = {10.64898/2026.08.31.747916},
url = {https://www.biorxiv.org/content/10.64898/2026.08.31.747916v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - QuickSeg: A fast, versatile and accurate algorithm for genomic copy number segmentation using dynamic programming
AU - B. Schlotmann
AU - F. Favero
AU - A. Locallo
AU - J. L. Weischenfeldt
PY - 2026
DA - 2026/08/31
PB - bioRxiv
DO - 10.64898/2026.08.31.747916
UR - https://www.biorxiv.org/content/10.64898/2026.08.31.747916v1
AB - Copy number alterations are among the most common genomic aberrations in cancer and their accurate identification relies on robust segmentation of sequencing read-depth signals. Existing segmentation methods typically balance computational efficiency against segmentation accuracy and remain sensitive to technical artifacts present in sequencing data. Here, we present QuickSeg, a fast and versatile methodology that uses an exact dynamic programming algorithm to detect copy number segments using median-based error function. Motivated by the observation that sequencing depth distributions contain a small but pervasive population of outlying observations, this approach provides increased robustness to technical noise while simultaneously reducing the computational complexity of the segmentation problem. Across whole-genome sequencing of cancer cohorts, using breakpoint-supported somatic copy number alterations, we demonstrate improved segmentation precision over two widely used baseline methods, Circular Binary Segmentation (CBS) and Piecewise Constant Fitting (PCF), across a broad range of sensitivity thresholds. QuickSeg also consistently outperformed both methods with respect to runtime and memory usage. Collectively, our results show that robust median-based optimization provides both biological and computational advantages for copy number segmentation, enabling accurate analysis of large sequencing cohorts with minimal computational requirements.
ER -