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BUSCO specifications

Information


Unique identifier OMICS_08894
Name BUSCO
Alternative name Benchmarking Universal Single-Copy Orthologs
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Evgeny M. Zdobnov

Publication for Benchmarking Universal Single-Copy Orthologs

BUSCO citations

 (414)
library_books

Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast

2018
BMC Genomics
PMCID: 5952469
PMID: 29764372
DOI: 10.1186/s12864-018-4751-5

[…] -ES (Lomsadze et al., 2014) was self-trained [] and Augustus was used with the training parameters for Neurospora crassa [].The genome assembly and gene prediction completeness was evaluated with the Benchmarking Universal Single-Copy Orthologs (BUSCO 3) software [] in genomic and proteomic modes, using the dataset for fungi []. The genomic mode was used with augustus trained on the genome of Neur […]

library_books

Evolutionary instability of CUG Leu in the genetic code of budding yeasts

2018
Nat Commun
PMCID: 5951914
PMID: 29760453
DOI: 10.1038/s41467-018-04374-7

[…] the site (Supplementary Fig. ). Counts of CUG codon occurrence in ORFs, in genes with HSPs, and in HSP regions (Supplementary Figs. , ) were calculated from the results of BLAST searches against the BUSCO Ascomycota ‘ancestral’ database.tRNA genes were predicted using tRNAscan-SE, with introns removed by our own Python code. In some Kluyveromyces species, the tLCAG gene was not predicted by tRNAs […]

library_books

Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution

2018
BMC Genomics
PMCID: 5941490
PMID: 29739321
DOI: 10.1186/s12864-018-4711-0

[…] rated using short-read technologies. Specifically, we assessed multiple approaches for assembling the Bambusicola genome from such data and evaluated the quality of our assembly using both a standard BUSCO analysis [] and an assessment of our ability to recover an independently generated set of curated ultraconserved elements (UCEs) from our genome assembly []. Given the interest in identifying se […]

library_books

Whole genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant

2018
GigaScience
PMCID: 5941149
PMID: 29722814
DOI: 10.1093/gigascience/giy044

[…] t of other birds, and the BUSCO benchmark. In this study, the draft genome assembled using MaSuRCA was selected because it generated dramatically longer scaffolds that displayed a decent score on the BUSCO benchmark and produced proper annotations for the predicted genes. Although scaffolds of the draft genome displayed some degree of fragmentation (Fig. ) and showed translocation (Fig. ) in certa […]

library_books

Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen fixing rhizobium symbioses

2018
Proc Natl Acad Sci U S A
PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115

[…] d in SI Appendix, Supplementary Methods). Validation of the final assemblies showed that 90–100% of the genomic reads mapped back to the assemblies (SI Appendix, Table S4), and 94–98% of CEGMA () and BUSCO () genes were detected (SI Appendix, Table S5). […]

library_books

Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty

2018
Nat Commun
PMCID: 5928047
PMID: 29712911
DOI: 10.1038/s41467-018-04136-5

[…] ementary Fig. , Supplementary Data ). These genomes were generated with different sequencing technologies, coverage, and gene prediction software. The completeness of these genomes was assessed using BUSCO (Supplementary Data , Supplementary Fig. ); 10 animal genomes showed percentages of missing genes above 15%, but five of them belong to animals that had suffered known genome reductions, while t […]

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BUSCO institution(s)
Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, Geneva, Switzerland

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