BUSCO: Assessing Genome Assembly and Annotation Completeness with Single-Copy Orthologs

With ever-lowering sequencing costs, genome sequencing projects have been initiated for a wide range of organisms, however the vast majority of genomes currently exist in the form of draft assemblies. Considering that an important driving force behind genome projects is the acquisition of a complete catalog of genes, an important task lies in assessing the integrity and completeness of the assembled genome. Although some indications of assembly quality may be gleaned from statistical measures, a key measure of assembly quality lies in its completeness in terms of the expected gene content. The identification of genes from many diverse species that are evolving under single-copy control defines such an evolutionarily-informed expectation regarding gene content. Selected from the major species clades of the OrthoDB catalog of orthologs, the Benchmarking Universal Single-Copy Orthologs (BUSCOs) defines sets of genes expected to be present in any newly-sequenced genome from the appropriate species clade. The BUSCO assessment tool, available from http://busco.ezlab.org, implements a computational pipeline to identify and classify matches from genome assemblies, annotated gene sets, or transcriptomes. This approach provides a novel and complementary metric to assess genome assembly quality, integrity and completeness that can be easily applied to draft genome assemblies even in the absence of any gene annotations. This facilitates informative comparisons and allows the quantification of iterative improvements to assemblies or annotations. BUSCO assessments therefore offer intuitive metrics, based on evolutionarily-informed expectations of gene content from hundreds of species, to gauge completeness of rapidly-accumulating genomic data.