Accurate long-read de novo assembly evaluation with Inspector

被引：88

作者：

Chen, Yu ^{[1
,2
]}

Zhang, Yixin ^{[3
]}

Wang, Amy Y. ^{[2
,4
]}

Gao, Min ^{[2
,5
]}

Chong, Zechen ^{[1
,2
]}

机构：

[1] Univ Alabama Birmingham, Heersink Sch Med, Dept Genet, Birmingham, AL 35294 USA

[2] Univ Alabama Birmingham, Heersink Sch Med, Informat Inst, Birmingham, AL 35294 USA

[3] Univ Alabama Birmingham, Coll Arts & Sci, Dept Comp Sci, Birmingham, AL 35294 USA

[4] Univ Alabama Birmingham, Heersink Sch Med, Dept Med, Div Gen Internal Med, Birmingham, AL 35294 USA

[5] Univ Alabama Birmingham, Heersink Sch Med, Dept Med, Div Cardiovasc Dis, Birmingham, AL 35233 USA

来源：

GENOME BIOLOGY | 2021年 / 22卷 / 01期

关键词：

De novo assembly; Long reads; Assembly evaluation; Assembly error; Genome assembly; GENOME ASSEMBLIES; SEQUENCE;

D O I：

10.1186/s13059-021-02527-4

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

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.

引用

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