Accurate long-read de novo assembly evaluation with Inspector

Genome Biology

Yixin Zhang¹  Yu Chen²  Zechen Chong²  Min Gao³  Amy Y. Wang⁴ 

[1] Department of Computer Science, College of Arts and Sciences, University of Alabama at Birmingham, 35294, Birmingham, AL, USA;Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, 35294, Birmingham, AL, USA;Informatics Institute, Heersink School of Medicine, University of Alabama at Birmingham, 35294, Birmingham, AL, USA;Informatics Institute, Heersink School of Medicine, University of Alabama at Birmingham, 35294, Birmingham, AL, USA;Department of Medicine, Division of Cardiovascular Disease, Heersink School of Medicine, University of Alabama at Birmingham, 35233, Birmingham, AL, USA;Informatics Institute, Heersink School of Medicine, University of Alabama at Birmingham, 35294, Birmingham, AL, USA;Department of Medicine, Division of General Internal Medicine, Heersink School of Medicine, University of Alabama at Birmingham, 35294, Birmingham, AL, USA;

关键词: De novo assembly;    Long reads;    Assembly evaluation;    Assembly error;    Genome assembly;   

DOI  :  10.1186/s13059-021-02527-4

来源: Springer

【 摘 要 】

Long-read de novo genome assembly continues to advance rapidly. However, there is a lack of effective tools to accurately evaluate the assembly results, especially for structural errors. We present Inspector, a reference-free long-read de novo assembly evaluator which faithfully reports types of errors and their precise locations. Notably, Inspector can correct the assembly errors based on consensus sequences derived from raw reads covering erroneous regions. Based on in silico and long-read assembly results from multiple long-read data and assemblers, we demonstrate that in addition to providing generic metrics, Inspector can accurately identify both large-scale and small-scale assembly errors.

【 授权许可】

CC BY