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Motivation: Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50.

Results: We propose a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content. We implemented the assessment procedure in open-source software, with sets of Benchmarking Universal Single-Copy Orthologs, named BUSCO.

Availability and implementation: Software implemented in Python and datasets available for download from http://busco.ezlab.org.

Contact: [email protected]

Supplementary information: Supplementary data are available at Bioinformatics online.

(C) Copyright Oxford University Press 2015.