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

LongTR ： 来自长读数的串联重复序列的遗传变异的全基因组分析。

• 发表时间: 2024 Jul 4
• 来源期刊: Genome Biol
• DOI: 10.1186/s13059-024-03319-2
• PMID: 38965568
• 文章类型: Journal Article
• 作者列表: Ziaei Jam H,Zook JM,Javadzadeh S,Park J,Sehgal A,Gymrek M

关键词: Long reads; Microsatellites; Tandem repeats

Mesh: Humans; Tandem Repeat Sequences; Genome, Human; Genetic Variation; Software; Sequence Analysis, DNA / methods; High-Throughput Nucleotide Sequencing / methods; Nanopore Sequencing / methods

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 .

摘要

串联重复在整个人类基因组中频繁出现，重复长度的变化与多种性状有关。最近长读取测序技术的改进有可能极大地改善串联重复分析，尤其是长时间或复杂的重复。这里,我们介绍LongTR,从PacBio和OxfordNanoporeTechnologies提供的高保真长读数中准确地串联重复基因型。LongTR可在https://github.com/gymorek-lab/longtr和https://zenodo.org/doi/10.5281/zenodo.11403979上免费获得。