Some users may experience unexpected lineage assignments when running BUSCO with SEPP v4.5.6 (this may concern users who installed BUSCO v6.0.0 from Conda before Dec. 2). This is due to a compatibility issue between the auto-lineage files and this newer version of SEPP.
The last BUSCO v6.0.0 on Conda pins SEPP to v4.5.5 by default. Make sure your installation is using SEPP 4.5.5 for auto-lineage compatibility, and reinstall from Conda if needed. (For the Docker image, no action is required).
The following protocol covers the various BUSCO running modes and workflows, setup, guidelines to interpret the results, and additional analyses, e.g., for building phylogenomic trees and visualizing syntenies using BUSCO results:
All publications: BUSCO: Assessing Genome Assembly and Annotation Completeness. Mathieu Seppey, Mosè Manni, Evgeny M. Zdobnov In: Kollmar M. (eds) Gene Prediction. Methods in Molecular Biology, vol 1962. Humana, New York, NY. 2019 doi.org/10.1007/978-1-4939-9173-0_14
BUSCO applications from quality assessments to gene prediction and phylogenomics. Robert M. Waterhouse, Mathieu Seppey, Felipe A. Simão, Mosè Manni, Panagiotis Ioannidis, Guennadi Klioutchnikov, Evgenia V. Kriventseva, and Evgeny M. Zdobnov Mol Biol Evol, published online Dec 6, 2017 doi: 10.1093/molbev/msx319
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Felipe A. Simão, Robert M. Waterhouse, Panagiotis Ioannidis, Evgenia V. Kriventseva, and Evgeny M. Zdobnov Bioinformatics, published online June 9, 2015 doi: 10.1093/bioinformatics/btv351
Copyright (c) 2015-2024, Evgeny Zdobnov (ez@ezlab.org)
Licensed under the MIT license. See LICENSE.md file.
BUSCOv5 - Benchmarking sets of Universal Single-Copy Orthologs.
For full documentation please consult the user guide: https://busco.ezlab.org/busco_userguide.html
⚠️ Important Notice: Auto-lineage Compatibility
Some users may experience unexpected lineage assignments when running BUSCO with SEPP v4.5.6 (this may concern users who installed BUSCO v6.0.0 from Conda before Dec. 2).
This is due to a compatibility issue between the auto-lineage files and this newer version of SEPP. The last BUSCO v6.0.0 on Conda pins SEPP to v4.5.5 by default. Make sure your installation is using SEPP 4.5.5 for auto-lineage compatibility, and reinstall from Conda if needed.
(For the Docker image, no action is required).
Installation
Conda
Conda installation instructions are in the userguide here: https://busco.ezlab.org/busco_userguide.html#conda-package
Docker
BUSCO is available through DockerHub - instructions here: https://busco.ezlab.org/busco_userguide.html#docker-image
Manual installation
Manual installation is possible, though it is important to validate each of the dependencies before running BUSCO. More details in the user guide: https://busco.ezlab.org/busco_userguide.html#manual-installation
Troubleshooting
To get help with BUSCO use:
busco -handpython3 scripts/generate_plot.py -hReport problems on the BUSCO issue board at https://gitlab.com/ezlab/busco/issues
How to cite BUSCO
Fredrik Tegenfeldt, Dmitry Kuznetsov, Mosè Manni, Matthew Berkeley, Evgeny M Zdobnov, Evgenia V Kriventseva, OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes. Nucleic Acids Research
For earlier versions, v4/v5 and odb_10 datasets:
Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM., BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Molecular Biology and Evolution
The following protocol covers the various BUSCO running modes and workflows, setup, guidelines to interpret the results, and additional analyses, e.g., for building phylogenomic trees and visualizing syntenies using BUSCO results:
Manni, M., Berkeley, M. R., Seppey, M., & Zdobnov, E. M. (2021). BUSCO: Assessing genomic data quality and beyond. Current Protocols
All publications:
BUSCO: Assessing Genome Assembly and Annotation Completeness. Mathieu Seppey, Mosè Manni, Evgeny M. Zdobnov In: Kollmar M. (eds) Gene Prediction. Methods in Molecular Biology, vol 1962. Humana, New York, NY. 2019 doi.org/10.1007/978-1-4939-9173-0_14
BUSCO applications from quality assessments to gene prediction and phylogenomics. Robert M. Waterhouse, Mathieu Seppey, Felipe A. Simão, Mosè Manni, Panagiotis Ioannidis, Guennadi Klioutchnikov, Evgenia V. Kriventseva, and Evgeny M. Zdobnov Mol Biol Evol, published online Dec 6, 2017 doi: 10.1093/molbev/msx319
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Felipe A. Simão, Robert M. Waterhouse, Panagiotis Ioannidis, Evgenia V. Kriventseva, and Evgeny M. Zdobnov Bioinformatics, published online June 9, 2015 doi: 10.1093/bioinformatics/btv351
Copyright (c) 2015-2024, Evgeny Zdobnov (ez@ezlab.org) Licensed under the MIT license. See LICENSE.md file.