from QC to gene prediction and phylogenomics
Based on evolutionarily-informed expectations of gene content of near-universal single-copy orthologs, BUSCO metric is complementary to technical metrics like N50.
BUSCO version 4 is released! BUSCO.v3 is still available.
If you ran analyses on eukaryotes using v4.0.0 and v4.0.1, please validate you result with v4.0.2 or higher, as the score may have been underestimated
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:v4.0.5_cv1
docker run -u $(id -u) -v $(pwd):/busco_wd ezlabgva/busco:v4.0.5_cv1
or through conda
conda install -c bioconda -c conda-forge busco=4.0.6
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=4.0.6 python=3.x
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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