Difference between revisions of "BUSCO"

Revision as of 23:22, 28 February 2018

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

@@ Line 63: / Line 63: @@
 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 ${HPC_BUSCO_DAT}/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.
+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.
 |}}
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