A survey of sequence-to-graph mapping algorithms in the pangenome era

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-05-22 DOI:10.1186/s13059-025-03606-6

Yingbo Cui, Chenchen Peng, Zeyu Xia, Canqun Yang, Yifei Guo

引用次数: 0

Abstract

A pangenome can reveal the genetic diversity across different individuals simultaneously. It offers a more comprehensive reference for genome analysis compared to a single linear genome that may introduce allele bias. Pangenomes are often represented as genome graphs, making sequence-to-graph mapping a fundamental task for pangenome construction and analysis. Numerous sequence-to-graph mapping algorithms have been developed over the past few years. Here, we provide a review of the advancements in sequence-to-graph mapping algorithms in the pangenome era. We also discuss the challenges and opportunities that arise in the context of pangenome graphs.

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泛基因组时代序列-图映射算法综述

泛基因组可以同时揭示不同个体之间的遗传多样性。相对于可能引入等位基因偏倚的单一线性基因组，它为基因组分析提供了更全面的参考。泛基因组通常被表示为基因组图，使得序列到图的绘制成为泛基因组构建和分析的基本任务。在过去的几年中，已经开发了许多序列到图的映射算法。在这里，我们提供了在泛基因组时代的序列到图映射算法的进展综述。我们还讨论了泛基因组图背景下出现的挑战和机遇。

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.