NASTRA: accurate analysis of short tandem repeat markers by nanopore sequencing with repeat-structure-aware algorithm.

IF 6.8 2区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Briefings in bioinformatics Pub Date : 2024-09-23 DOI:10.1093/bib/bbae472

Zilin Ren, Jiarong Zhang, Yixiang Zhang, Tingting Yang, Pingping Sun, Jiguo Xue, Xiaochen Bo, Bo Zhou, Jiangwei Yan, Ming Ni

引用次数: 0

Abstract

Short-tandem repeats (STRs) are the type of genetic markers extensively utilized in biomedical and forensic applications. Due to sequencing noise in nanopore sequencing, accurate analysis methods are lacking. We developed NASTRA, an innovative tool for Nanopore Autosomal Short Tandem Repeat Analysis, which overcomes traditional database-based methods' limitations and provides a precise germline analysis of STR genetic markers without the need for allele sequence reference. Demonstrating high accuracy in cell line authentication testing and paternity testing, NASTRA significantly surpasses existing methods in both speed and accuracy. This advancement makes it a promising solution for rapid cell line authentication and kinship testing, highlighting the potential of nanopore sequencing for in-field applications.

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NASTRA：利用重复结构感知算法通过纳米孔测序准确分析短串联重复标记。

短串联重复序列（STR）是生物医学和法医应用中广泛使用的一类遗传标记。由于纳米孔测序存在测序噪声，因此缺乏精确的分析方法。我们开发了一种用于纳米孔常染色体短串联重复序列分析的创新工具 NASTRA，它克服了传统的基于数据库的方法的局限性，无需等位基因序列参考就能对 STR 遗传标记进行精确的种系分析。NASTRA 在细胞系鉴定测试和亲子鉴定中表现出很高的准确性，在速度和准确性上都大大超过了现有的方法。这一进步使其成为快速细胞系鉴定和亲缘关系测试的理想解决方案，凸显了纳米孔测序在现场应用中的潜力。

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

Briefings in bioinformatics 生物-生化研究方法

CiteScore

13.20

自引率

13.70%

发文量

549

审稿时长

6 months

期刊介绍： Briefings in Bioinformatics is an international journal serving as a platform for researchers and educators in the life sciences. It also appeals to mathematicians, statisticians, and computer scientists applying their expertise to biological challenges. The journal focuses on reviews tailored for users of databases and analytical tools in contemporary genetics, molecular and systems biology. It stands out by offering practical assistance and guidance to non-specialists in computerized methodologies. Covering a wide range from introductory concepts to specific protocols and analyses, the papers address bacterial, plant, fungal, animal, and human data. The journal's detailed subject areas include genetic studies of phenotypes and genotypes, mapping, DNA sequencing, expression profiling, gene expression studies, microarrays, alignment methods, protein profiles and HMMs, lipids, metabolic and signaling pathways, structure determination and function prediction, phylogenetic studies, and education and training.