BUSCO

Description

busco website  

Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

Required Modules

Serial

• busco

System Variables

• HPC_{{#uppercase:busco}}_DIR - installation directory

Additional Information

Busco uses a config file which needs to be copied and modified to your needs.

$ cp $HPC_BUSCO_CONF/config.ini /home/username/busco
$ export BUSCO_CONFIG_FILE=/home/username/busco
$ run_BUSCO.py

Datasets are located in /ufrc/data/reference/busco/

Available datasets:

• arthropoda
• bacteria
• eukaryota
• fungi
• metazoa
• vertebrata

Example of busco run with metazoa dataset:

busco -f -in target.fa -o SAMPLE -l ${HPC_BUSCO_DAT}/metazoa -m genome

To allow busco to retrain the augustus dataset create a local augustus directory, set $AUGUSTUS_CONFIG_PATH variable to that path, and copy the dataset for the organism in question to your local directory. as explained on the Augustus page.

Citation

If you publish research that uses busco you have to cite it as follows:

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