BUSCO v3 provides quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness, based on evolutionarily-informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB v9.

BUSCO assessments are implemented in open-source software, with a large selection of lineage-specific sets of Benchmarking Universal Single-Copy Orthologs. These conserved orthologs are ideal candidates for large-scale phylogenomics studies, and the annotated BUSCO gene models built during genome assessments provide a comprehensive gene predictor training set for use as part of genome annotation pipelines.

• Download the BUSCO v3 source code from our GitLab project:     http://gitlab.com/ezlab/busco
• Download the BUSCO v3 user guide:     BUSCO_userguide.pdf
• Run BUSCO v3 using our Ubuntu virtual machine, with all dependencies included:     BUSCO_UBUNTU_VM.ova
  
  - For help related to running the VM, please refer to Ubuntu, VirtualBox and OSboxes.

BUSCO applications from quality assessments to gene prediction and phylogenomics.
Robert M. Waterhouse, Mathieu Seppey, Felipe A. Simão, Mose Manni, Panagiotis Ioannidis, Guennadi Klioutchnikov, Evgenia V. Kriventseva, and Evgeny M. Zdobnov
Mol Biol Evol, published online Dec 6, 2017 | Abstract | Full Text PDF | doi: 10.1093/molbev/msx319

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Felipe A. Simão, Robert M. Waterhouse, Panagiotis Ioannidis, Evgenia V. Kriventseva, and Evgeny M. Zdobnov
Bioinformatics, published online June 9, 2015 | Abstract | Full Text PDF | doi: 10.1093/bioinformatics/btv351
Supplementary Online Materials: SOM

BUSCO v1 website for archived code and datasets:    http://busco.ezlab.org/v1