Topsicle: a method for estimating telomere length from whole genome long-read sequencing data

IF 10.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Linh Nguyen, Jae Young Choi
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引用次数: 0

Abstract

Telomeres protect chromosome ends and their length varies significantly between organisms. Because telomere length variation is associated with various biomedical and eco-evolutionary phenotypes, many biological fields are interested in understanding its biological significance. Here, we introduce Topsicle, a computational method that estimates telomere length from whole genome long-read sequencing data using k-mer and change-point detection analysis. Simulations show Topsicle is robust to sequencing errors and coverage. Application of Topsicle to plant and human cancer cells shows high accuracy and comparable results to direct telomere length measurements. We predict Topsicle will be a useful tool for studying telomere biology.
从全基因组长读测序数据估计端粒长度的方法
端粒保护染色体末端,其长度在不同生物体之间差别很大。由于端粒长度变异与各种生物医学和生态进化表型有关,许多生物学领域都对了解其生物学意义感兴趣。在这里,我们介绍了Topsicle,这是一种利用k-mer和变化点检测分析从全基因组长读测序数据估计端粒长度的计算方法。仿真结果表明,Topsicle对序列误差和覆盖具有较强的鲁棒性。Topsicle在植物和人类癌细胞上的应用显示了与直接端粒长度测量相比的高精度和可比较的结果。我们预测Topsicle将成为研究端粒生物学的有用工具。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Genome Biology
Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
21.00
自引率
3.30%
发文量
241
审稿时长
2 months
期刊介绍: Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.
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