BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes
Open accessAbstract
Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly procedures and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs. Here, we present new functionalities and major improvements of the BUSCO software, as well as the renewal and expansion of the underlying data sets in sync with the OrthoDB v10 release. Among the major novelties, BUSCO now enables phylogenetic placement of the input sequence to automatically select the most appropriate BUSCO data set for the assessment, allowing the analysis of metagenome-assembled genomes of unknown origin. A newly introduced genome workflow increases the efficiency and runtimes especially on large eukaryotic genomes. BUSCO is the only tool capable of assessing both eukaryotic and prokaryotic species, and can be applied to various data types, from genome assemblies and metagenomic bins, to transcriptomes and gene sets.
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TOGA annotations have a higher BUSCO completeness score for 97% of Ensembl species and 91.5% of NCBI species, increasing annotation completeness of conserved genes by an average of 4.1% or ~377 genes (Ensembl) and 0.7% or ~64 genes (NCBI).
“TOGA annotations have a higher completeness score for 97% (Ensembl) and 91.5% (NCBI) of the species (Fig. 3A,B, Tables S6–S7), increasing annotation completeness of conserved genes by an average of 4.1% or ~377 genes (Ensembl) and 0.7% or ~64 genes (NCBI) (fig. S30).”
From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [23]
The Upgrade of Data Sets and Benchmark of Predictions sections describe BUSCO scores as estimates of genome and gene-set completeness, supporting the use of BUSCO as the assessment method. Our copy does not report a TOGA comparison with Ensembl or NCBI annotations, or the claimed percentages and gene counts. No page numbers are available in our copy. (LLM, conf=0.86)
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Influential
- Authors
- Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A., & Zdobnov, E. M.
- Affiliations
- University of Geneva (CH)
- Corresponding author
- Zdobnov, Evgeny M
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2021-07-28
- Volume
- 38
- Issue
- 10
- Pages
- 4647-4654
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC8476166
- OpenAlex
- W3175616293
- Cited by
- 6,187
- References
- 4
- Citations by year
- 2026: 1415 · 2025: 1648 · 2024: 1460 · 2023: 1109 · 2022: 498 · 2021: 56
- FWCI
- 254.11
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Molecular Biology and Evolution (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- arXiv (Cornell University) (submittedVersion)
- Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
- arXiv (Cornell University)
- Funders
- Swiss National Science Foundation (310030_189062)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
- Keywords
- BUSCO, single-copy orthologs, OrthoDB, metagenome-assembled genomes, phylogenetic placement, eukaryotic genomes, prokaryotic genomes, viral genome, genome assembly quality, transcriptome
- MeSH terms
- Phylogeny, Genome, Viral, Genomics, Eukaryota, Workflow
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