DEGAP: Dynamic elongation of a genome assembly path

文献类型： 外文期刊

第一作者： Huang, Yicheng

作者： Huang, Yicheng;Su, Handong;Xiong, Lizhong;Zhang, Jianwei;Wang, Ziyuan;Schmidt, Monica A.;Su, Handong

作者机构：

关键词： gap closure; genome assembler; HiFi reads

期刊名称：BRIEFINGS IN BIOINFORMATICS （ 影响因子：6.8； 五年影响因子：7.9 ）

ISSN： 1467-5463

年卷期： 2024 年 25 卷 3 期

页码：

收录情况： SCI

摘要： Genome assembly remains to be a major task in genomic research. Despite the development over the past decades of different assembly software programs and algorithms, it is still a great challenge to assemble a complete genome without any gaps. With the latest DNA circular consensus sequencing (CCS) technology, several assembly programs can now build a genome from raw sequencing data to contigs; however, some complex sequence regions remain as unresolved gaps. Here, we present a novel gap-filling software, DEGAP (Dynamic Elongation of a Genome Assembly Path), that resolves gap regions by utilizing the dual advantages of accuracy and length of high-fidelity (HiFi) reads. DEGAP identifies differences between reads and provides 'GapFiller' or 'CtgLinker' modes to eliminate or shorten gaps in genomes. DEGAP adopts an iterative elongation strategy that automatically and dynamically adjusts parameters according to three complexity factors affecting the genome to determine the optimal extension path. DEGAP has already been successfully applied to decipher complex genomic regions in several projects and may be widely employed to generate more gap-free genomes.

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