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 metazoa -m genome

If you encounter an cannot write to to the Augustus config path error make sure you set the $AUGUSTUS_CONFIG_PATH variable 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