Work

TD-TSPS: A hybrid strategy method for TD detection based on two-step progressive segmentation

Year: 2026

Type: software-paper

Abstract: Tandem duplication (TD) represents a crucial type of structural variations within the human genome. When the sequencing depth is low, TD signal at each single nucleotide position becomes more indistinct. So the detection of TDs under low coverage remains a challenging task. This paper proposes a method called TD-TSPS (Two-Step Progressive Segmentation for TD detection) on whole genome sequencing data. A two-step progressive segmentation strategy is employed to divide the genome into continuous and similar bins. Additionally, it integrates split read and paired-end mapping strategies to refine TD regions. Performance tests on simulated and real datasets show that TD-TSPS achieves a good F1-score. Therefore, it can be used as an effective tool for TDs detection.

Source: SoftwareX

DOI: 10.1016/j.softx.2025.102499

Authors: Yuxi Zhang, Jinxin Dong, Hua Jiang, Ruchao Du, Ranran Sun

Institution: Liaocheng University

Language: English

Topic: Genomic variations and chromosomal abnormalities

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $1,200

Funder: Ministry of Industry and Information Technology of the People's Republic of China