Difference between revisions of "BUSCO"
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | Datasets are located in / | + | Datasets are located in /ufrc/data/reference/busco/ |
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Example of busco run with metazoa dataset: | Example of busco run with metazoa dataset: | ||
busco -f -in target.fa -o SAMPLE -l metazoa -m genome | 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. | ||
|}} | |}} | ||
<!--PBS scripts--> | <!--PBS scripts--> | ||
Revision as of 22:18, 25 January 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
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