BUSCO v2: Assessing Genome Assembly and Annotation Completeness Withbenchmarking Universal Single-Copy Orthologs

With the ever-increasing accessibility of sequencing, genome 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 motivation behind genome projects lies in the acquisition of a complete catalog of genes, it is vital to assess the integrity and completeness of the assembled genome. Although 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. Genes evolving under single-copy control across many diverse species provide an evolutionarily-informed expectation regarding the 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/v2/ implements a computational pipeline to identify and classify matches from genome assemblies, annotated gene sets, or transcriptomes. With the most recent update, BUSCO now contains datasets derived from over 40 different clades, spanning all domains of life. The BUSCO approach can be easily applied to draft genome or transcriptome 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 complementary and intuitive metrics, based on evolutionarily-informed expectations of gene content from hundreds of species, to gauge completeness of rapidly-accumulating genomic data.