Genome assembly and quality · Software
BUSCO
Assesses completeness of genome assemblies, gene sets, and transcriptomes using universal single-copy orthologs.
What BUSCO is
BUSCO (Benchmarking Universal Single-Copy Orthologs) is a bioinformatics tool developed by Evgeny Zdobnov's group at the University of Geneva and the Swiss Institute of Bioinformatics (SIB). It measures the completeness and quality of genome assemblies, annotated gene sets, and transcriptomes by evaluating them against sets of near-universal, single-copy orthologous genes.
Assembly and annotation projects often rely on basic structural statistics like N50 that reflect continuity rather than biological completeness. BUSCO provides an evolutionarily informed metric based on expected gene content across diverse taxonomic lineages, helping researchers quantify missing, duplicated, or fragmented genes in eukaryotic, prokaryotic, and viral genomic data.
The tool works in conjunction with curated lineage datasets derived from OrthoDB. Researchers can use BUSCO scores for quality control benchmarking, guiding gene prediction, building phylogenomic trees, and conducting comparative synteny analyses.
How it works
BUSCO takes sequence inputs in the form of whole genomes, transcriptomes, or protein sets and compares them against lineage-specific profile datasets derived from OrthoDB. The tool identifies candidate orthologous regions and evaluates them to determine whether expected single-copy orthologs are present as single copies, duplicated, fragmented, or missing.
Depending on the configuration and data type, the assessment workflow can employ different underlying annotation and search pipelines, including Metaeuk, BLAST combined with Augustus, or Miniprot (which serves as the default pipeline for eukaryota and an option for prokaryota). For genome mode assessments, it can also calculate assembly statistics and evaluate scaffold sequence composition.
Key facts
- Current version
- 6.1.0
- Input modes
- genome, protein, transcriptome
- Underlying lineage data
- OrthoDB (including OrthoDB v10 and OrthoDB v12)
- Supported pipelines
- Miniprot, Metaeuk, Augustus with BLAST
- Command-line interface
- busco
What you can use it for
- Genome assembly quality control
- Quantify the gene completeness, fragmentation, and duplication of newly assembled eukaryotic, prokaryotic, or viral genomes.
- Transcriptome completeness assessment
- Evaluate de novo or reference-guided transcriptome assemblies to ensure expected core orthologous transcripts have been recovered.
- Protein set validation
- Assess whether predicted proteomes or annotated gene sets represent a complete set of expected lineage-specific genes.
- Phylogenomic and synteny studies
- Use identified single-copy orthologs and their genomic arrangements across lineages to reconstruct phylogenomic trees and examine synteny.
Run it here
Ask the research agent and it runs BUSCO as a job on a dedicated machine, then reads the results back to you. Nothing to install, and it keeps running if you close the page.
Try asking
“Run BUSCO on my assembly with the bacteria_odb12 lineage and summarise completeness.”
Strengths and limits
Good at
- Provides an evolutionarily informed assessment of gene completeness that complements continuity metrics such as N50.
- Covers multiple taxonomic domains, offering lineage datasets spanning eukaryota, prokaryota, and viruses.
- Supports multiple execution pipelines, including Miniprot, Metaeuk, and Augustus.
- Automatically manages the selection and download of required lineage datasets.
Watch out for
- Requires manual validation of individual dependencies when installed without container or package managers.
- Relies on pre-computed OrthoDB lineage datasets that must correspond to the appropriate taxonomic lineage of the sample.
Questions
Can I run BUSCO online without installing it?
Ask the research agent and it runs BUSCO as a job on a dedicated machine, then reads the results back to you. Nothing to install, and it keeps running if you close the page.
What licence is BUSCO under?
Software MIT; lineage datasets CC BY-ND 4.0. The terms are published at https://busco.ezlab.org/.
What input data types can BUSCO process?
BUSCO supports three primary modes: 'genome' for assembled genomic sequences, 'transcriptome' for transcript assemblies, and 'protein' for translated protein sequence sets.
Which lineage datasets does BUSCO use?
BUSCO uses lineage datasets derived from OrthoDB, including OrthoDB v12 (odb12.2 and odb12) and earlier OrthoDB v10 releases, spanning eukaryota, prokaryota, and viruses.
Can BUSCO be run in an offline environment?
Yes. BUSCO includes an '--offline' flag to prevent automatic network requests, provided the required lineage datasets have been downloaded in advance.
How can I see all available lineage datasets?
You can display the full list of available lineage datasets by executing the command 'busco --list-datasets'.
How to cite it
Tegenfeldt F., Kuznetsov D., Manni M., Berkeley M., Zdobnov E.M., Kriventseva E.V. OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes. Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D516–D522, https://doi.org/10.1093/nar/gkae987
Written from BUSCO's own README and project page. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.