BUSCO applications from quality assessments to gene prediction and phylogenomics
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Abstract
Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic data sets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). The latest software release implements a complete refactoring of the code to make it more flexible and extendable to facilitate high-throughput assessments. The original six lineage assessment data sets have been updated with improved species sampling, 34 new subsets have been built for vertebrates, arthropods, fungi, and prokaryotes that greatly enhance resolution, and data sets are now also available for nematodes, protists, and plants. Here, we present BUSCO v3 with example analyses that highlight the wide-ranging utility of BUSCO assessments, which extend beyond quality control of genomics data sets to applications in comparative genomics analyses, gene predictor training, metagenomics, and phylogenomics.
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The assembly quality of HGFv1 was evaluated with BUSCO v3, LAI, and RNA-seq reads mapping.
“The assembly quality of HGFv1 was evaluated with BUSCO v3 (Waterhouse et al. 2018), LAI (LTR assembly index) (Ou et al. 2018), and RNA-seq reads mapping (Darris et al. 2015).”
From Genomic Analyses Unveil Helmeted Guinea Fowl (<i>Numida meleagris</i>) Domestication in West Africa (2021) · cites this paper as Waterhouse et al. 2018
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- Authors
- Waterhouse, R. M., Seppey, M., Simão, F. A., Manni, M., Ioannidis, P., Klioutchnikov, G., Kriventseva, E. V., & Zdobnov, E. M.
- Affiliations
- University of Geneva (CH)
- Corresponding author
- Zdobnov, Evgeny M
- ORCID
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-12-06
- Volume
- 35
- Issue
- 3
- Pages
- 543-548
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC5850278
- OpenAlex
- W2951257985
- Cited by
- 2,214
- References
- 31
- Citations by year
- 2026: 117 · 2025: 174 · 2024: 198 · 2023: 206 · 2022: 320 · 2021: 433 · 2020: 391 · 2019: 288 · 2018: 85 · 2017: 1
- FWCI
- 87.86
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- Locations
- Molecular Biology and Evolution (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- SERVAL (Université de Lausanne) (publishedVersion, other-oa)
- IRIS (submittedVersion, cc-by)
- Funders
- National Science Foundation (PP00P3_170664)
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (170664, 143936)
- Université de Genève
- 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 › Fractal and DNA sequence analysis
- Keywords
- BUSCO, sequencing quality control, phylogenomics, comparative genomics, metagenomics
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