基于长读长的串联重复序列遗传变异全基因组分析。

Genome-wide profiling of genetic variation at tandem repeat from long reads.

作者信息

Jam Helyaneh Ziaei, Zook Justin M, Javadzadeh Sara, Park Jonghun, Sehgal Aarushi, Gymrek Melissa

机构信息

Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.

Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD, USA.

出版信息

bioRxiv. 2024 Jan 23:2024.01.20.576266. doi: 10.1101/2024.01.20.576266.

DOI:10.1101/2024.01.20.576266

PMID:38328152

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10849534/

Abstract

Tandem repeats are frequent across the human genome, and variation in repeat length has been linked to a variety of traits. Recent improvements in long read sequencing technologies have the potential to greatly improve TR analysis, especially for long or complex repeats. Here we introduce LongTR, which accurately genotypes tandem repeats from high fidelity long reads available from both PacBio and Oxford Nanopore Technologies. LongTR is freely available at https://github.com/gymrek-lab/longtr.

摘要

串联重复序列在人类基因组中很常见，重复长度的变异与多种性状有关。长读长测序技术的最新进展有可能极大地改善串联重复序列分析，特别是对于长的或复杂的重复序列。在这里，我们介绍LongTR，它可以从PacBio和Oxford Nanopore Technologies提供的高保真长读长中准确地对串联重复序列进行基因分型。LongTR可在https://github.com/gymrek-lab/longtr上免费获取。