Accurate long-read de novo assembly evaluation with Inspector

• Published in: Genome Biology Vol. 22; no. 1; p. 312
• Main Authors: Chen, Yu, Zhang, Yixin, Wang, Amy Y, Gao, Min, Chong, Zechen
• Format: Journal Article
• Language: English
• Published: England BioMed Central 14-11-2021; BMC
• Subjects: Accuracy; Algorithms; Assembly error; Assembly evaluation; De novo assembly; Error correction & detection; Genome; Genome assembly; Genomes; Haplotypes; High-Throughput Nucleotide Sequencing - methods; Humans; Long reads; Method; Sequence Analysis, DNA - methods; Whole Genome Sequencing - methods; Assembly error; Genome assembly; Long reads; Assembly evaluation; De novo assembly
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-021-02527-4

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.