BUSCO is a benchmarking tool used to assess the completeness of genome assemblies, gene sets, and transcriptomes by evaluating the presence of expected single-copy orthologs. It provides quantitative measures of gene content completeness, which is crucial for genomics data quality control. BUSCO assessments have been widely adopted in genomics research for data quality control and are also used for building gene predictor training sets, selecting high-quality reference species for comparative analyses, and identifying reliable phylogenomics markers. The tool is based on evolutionary expectations of gene content, using orthologous groups with single-copy orthologs in most species for each major lineage. BUSCO datasets are derived from OrthoDB and have been updated to include more lineages and provide higher resolution. BUSCO v2 and v3 have improved the tool's performance and provided more comprehensive information on analysis progress and error reporting. BUSCO assessments can identify complete, duplicated, fragmented, and missing genes, allowing users to compare their data to gold-standard model organisms or other closely-related species. BUSCO is also used to assess transcriptomes and annotated gene sets, making it a versatile tool for genomics research. The tool has been applied in various studies to improve genome assemblies, assess genome quality, and identify reliable phylogenomics markers. BUSCO assessments have shown that genome assemblies with higher BUSCO completeness scores are more accurate and complete. The tool is also used to train gene prediction algorithms, such as Augustus, using BUSCO-trained parameters, which can improve the accuracy of gene model predictions. BUSCO has been used in comparative genomic analyses to select the most complete genomic resources for studies, and in phylogenomics to identify reliable single-copy markers for inferring species phylogeny. The tool has been applied in various studies to improve the accuracy of phylogenetic analyses and to identify reliable markers for large-scale phylogenomics studies. Overall, BUSCO is a valuable tool for genomics research, providing a quantitative measure of genome assembly and annotation completeness, and is widely used in the genomics community.BUSCO is a benchmarking tool used to assess the completeness of genome assemblies, gene sets, and transcriptomes by evaluating the presence of expected single-copy orthologs. It provides quantitative measures of gene content completeness, which is crucial for genomics data quality control. BUSCO assessments have been widely adopted in genomics research for data quality control and are also used for building gene predictor training sets, selecting high-quality reference species for comparative analyses, and identifying reliable phylogenomics markers. The tool is based on evolutionary expectations of gene content, using orthologous groups with single-copy orthologs in most species for each major lineage. BUSCO datasets are derived from OrthoDB and have been updated to include more lineages and provide higher resolution. BUSCO v2 and v3 have improved the tool's performance and provided more comprehensive information on analysis progress and error reporting. BUSCO assessments can identify complete, duplicated, fragmented, and missing genes, allowing users to compare their data to gold-standard model organisms or other closely-related species. BUSCO is also used to assess transcriptomes and annotated gene sets, making it a versatile tool for genomics research. The tool has been applied in various studies to improve genome assemblies, assess genome quality, and identify reliable phylogenomics markers. BUSCO assessments have shown that genome assemblies with higher BUSCO completeness scores are more accurate and complete. The tool is also used to train gene prediction algorithms, such as Augustus, using BUSCO-trained parameters, which can improve the accuracy of gene model predictions. BUSCO has been used in comparative genomic analyses to select the most complete genomic resources for studies, and in phylogenomics to identify reliable single-copy markers for inferring species phylogeny. The tool has been applied in various studies to improve the accuracy of phylogenetic analyses and to identify reliable markers for large-scale phylogenomics studies. Overall, BUSCO is a valuable tool for genomics research, providing a quantitative measure of genome assembly and annotation completeness, and is widely used in the genomics community.