AlfaPang: alignment free algorithm for pangenome graph construction.

IF 1.5 4区生物学 Q4 BIOCHEMICAL RESEARCH METHODS

Algorithms for Molecular Biology Pub Date : 2025-05-15 DOI:10.1186/s13015-025-00277-7

Adam Cicherski, Anna Lisiecka, Norbert Dojer

引用次数: 0

Abstract

The success of pangenome-based approaches to genomics analysis depends largely on the existence of efficient methods for constructing pangenome graphs that are applicable to large genome collections. In the current paper we present AlfaPang, a new pangenome graph building algorithm. AlfaPang is based on a novel alignment-free approach that allows to construct pangenome graphs using significantly less computational resources than state-of-the-art tools. The code of AlfaPang is freely available at https://github.com/AdamCicherski/AlfaPang .

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AlfaPang：用于泛基因组图构建的无对齐算法。

基于泛基因组的基因组学分析方法的成功在很大程度上取决于构建适用于大型基因组集合的泛基因组图的有效方法的存在。本文提出了一种新的泛基因组图谱构建算法AlfaPang。AlfaPang基于一种新颖的无对齐方法，可以使用比最先进的工具更少的计算资源来构建泛基因组图。AlfaPang的代码可以在https://github.com/AdamCicherski/AlfaPang上免费获得。

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

Algorithms for Molecular Biology 生物-生化研究方法

CiteScore

2.40

自引率

10.00%

发文量

审稿时长

>12 weeks

期刊介绍： Algorithms for Molecular Biology publishes articles on novel algorithms for biological sequence and structure analysis, phylogeny reconstruction, and combinatorial algorithms and machine learning. Areas of interest include but are not limited to: algorithms for RNA and protein structure analysis, gene prediction and genome analysis, comparative sequence analysis and alignment, phylogeny, gene expression, machine learning, and combinatorial algorithms. Where appropriate, manuscripts should describe applications to real-world data. However, pure algorithm papers are also welcome if future applications to biological data are to be expected, or if they address complexity or approximation issues of novel computational problems in molecular biology. Articles about novel software tools will be considered for publication if they contain some algorithmically interesting aspects.