Difference between revisions of "BUSCO"
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
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| + | Busco uses a config file which needs to be copied and modified to your needs. | ||
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| + | $ 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/ | Datasets are located in /ufrc/data/reference/busco/ | ||
Revision as of 15:58, 13 July 2017
Description
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