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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 4.1.3 is the current stable version!

https://gitlab.com/ezlab/busco/-/tags/4.1.3

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:v4.1.3_cv1
docker run -u $(id -u) -v $(pwd):/busco_wd ezlabgva/busco:v4.1.3_cv1

..more >> ..source >>

or through conda

conda install -c bioconda -c conda-forge busco=4.1.3 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=4.1.3 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

..more >>

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 download them manually and see a list with the number of marker genes.

Earlier versions: v3, v2, v1

Documentation and support

User guide Issues board

You 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

more & stats >>

"Core" genes

BUSCO sampling space adapted from