from QC to gene prediction and phylogenomics
BUSCO version 5 beta is released!
The source code is available on gitlab. A conda package and corresponding containers will follow soon.
We welcome feedback and bug reports on https://gitlab.com/ezlab/busco/-/issues
While still using the odb10 datasets, the changes will affect the scores
BUSCO version 4.1.2 is the current stable version!
https://gitlab.com/ezlab/busco/-/tags/4.1.2
And BUSCO.v3 is still available.
Based on evolutionarily-informed expectations of gene content of near-universal single-copy orthologs, BUSCO metric is complementary to technical metrics like N50.
Availability
- Git source code
- Docker container
- Conda package
New in v4
- Bacteria & archaea revised
- Auto-lineage selection
- Automated download of datasets
vs CheckM
- Scores eukaryotes and prokaryotes
- Can run on a laptop
- Better resolution, less overestimates
Obtain BUSCO
Read the user guide for details.
docker pull ezlabgva/busco:v4.1.2_cv1
docker run -u $(id -u) -v $(pwd):/busco_wd ezlabgva/busco:v4.1.2_cv1
or through conda
conda install -c bioconda -c conda-forge busco=4.1.2 augustus=3.3.3
conda activate base
or through conda by creating a new environment (also try this if you encounter problems with the command above)
conda create -n your_env_name -c bioconda -c conda-forge busco=4.1.2 python=3.x augustus=3.3.3
conda activate your_env_name
or
git clone https://gitlab.com/ezlab/busco.git
https://gitlab.com/ezlab/busco/-/archive/master/busco-master.zip
The BUSCO software now directly downloads the necessary datasets, specified by the user or automatically selected.
To display all available datasets
busco --list-datasets
You can also select and download them manually and see a list with the number of marker genes.
Documentation and support
User guide Issues boardYou can also write to: support[at]orthodb.org.
Cite us
Seppey M., Manni M., Zdobnov E.M. (2019) BUSCO: Assessing Genome Assembly and Annotation Completeness. 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. PMID:31020564
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