LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2024-07-04 DOI:10.1186/s13059-024-03319-2

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

引用次数: 0

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 tandem repeat 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 and https://zenodo.org/doi/10.5281/zenodo.11403979 .

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LongTR：利用长读数对串联重复序列上的遗传变异进行全基因组剖析

人类基因组中经常出现串联重复序列，重复序列长度的变化与多种性状有关。最近长读数测序技术的改进有可能极大地改善串联重复序列分析，尤其是长重复序列或复杂重复序列的分析。在这里，我们介绍 LongTR，它能利用 PacBio 和牛津纳米孔技术公司提供的高保真长读数对串联重复序列进行准确的基因分型。LongTR 可在 https://github.com/gymrek-lab/longtr 和 https://zenodo.org/doi/10.5281/zenodo.11403979 免费获取。

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 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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