compleasm: a faster and more accurate reimplementation of BUSCO

• Published in: Bioinformatics (Oxford, England) Vol. 39; no. 10
• Main Authors: Huang, Neng, Li, Heng
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 03.10.2023
• Subjects: Applications Note; Benchmarking; Genome; Genomics; Humans; Molecular Sequence Annotation
• ISSN: 1367-4811; 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btad595

Abstract Motivation Evaluating the gene completeness is critical to measuring the quality of a genome assembly. An incomplete assembly can lead to errors in gene predictions, annotation, and other downstream analyses. Benchmarking Universal Single-Copy Orthologs (BUSCO) is a widely used tool for assessing the completeness of genome assembly by testing the presence of a set of single-copy orthologs conserved across a wide range of taxa. However, BUSCO is slow particularly for large genome assemblies. It is cumbersome to apply BUSCO to a large number of assemblies. Results Here, we present compleasm, an efficient tool for assessing the completeness of genome assemblies. Compleasm utilizes the miniprot protein-to-genome aligner and the conserved orthologous genes from BUSCO. It is 14 times faster than BUSCO for human assemblies and reports a more accurate completeness of 99.6% than BUSCO’s 95.7%, which is in close agreement with the annotation completeness of 99.5% for T2T-CHM13. Availability and implementation https://github.com/huangnengCSU/compleasm.