CloseRead：一种用于评估免疫球蛋白位点组装错误的工具，应用于脊椎动物长读基因组组装

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-05-20 DOI:10.1186/s13059-025-03594-7

Yixin Zhu, Corey Watson, Yana Safonova, Matt Pennell, Anton Bankevich

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引用次数: 0

摘要

尽管长读测序技术取得了巨大的进步，但一些结构复杂和重复序列丰富的基因组区域的组装仍然具有挑战性。此外，我们缺乏评估本地装配质量的工具，这使得识别问题和评估进展变得困难。在这里，我们开发了一种新的方法“CloseRead”，用于可视化本地装配质量和使用多个指标诊断错误。我们应用CloseRead来评估免疫球蛋白位点（结构复杂区域的典型案例）在74种最先进的脊椎动物基因组中的组装情况。然后，我们证明了靶向的局部重组可以纠正CloseRead识别的特定错误，突出了基因组组装迭代方法的价值。

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CloseRead: a tool for assessing assembly errors in immunoglobulin loci applied to vertebrate long-read genome assemblies

Despite tremendous advances in long-read sequencing, some structurally complex and repeat-rich genomic regions remain challenging to assemble. Furthermore, we lack tools to assess local assembly quality, making it hard to identify problems and assess progress. Here we develop a new approach “CloseRead” for visualizing local assembly quality and diagnosing errors using multiple metrics. We apply CloseRead to evaluate how well immunoglobulin loci, paradigmatic cases of structurally complex regions, are assembled in 74 state-of-the-art vertebrate genomes. We then show that targeted, local re-assembly can correct the specific errors identified by CloseRead, highlighting the value of an iterative approach to genome assembly.

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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.