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

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Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing (2016, methodology): “Furthermore, since the assembly contains both haplotypes (i.e. primary contigs and haplotigs), the vast majority of BUSCO genes (877) were found to be duplicated in the assemblies showing that the majority of the gene space was phased by the diploid assembly.”
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies (2020, methodology): “For measuring completeness and false duplications, near-universal single-copy orthologs (BUSCOs) [16] have been widely used to evaluate the gene content of assemblies.”
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm (2021, methodology): “BUSCO 24 is a popular tool for evaluating gene completeness.”