Difference between revisions of "BUSCO"

From UFRC
Jump to navigation Jump to search
m (Text replacement - "/ufrc/data/reference" to "/data/reference")
Line 50: Line 50:
  
  
Datasets are located in /ufrc/data/reference/busco/
+
Datasets are located in /data/reference/busco/
  
  
Line 61: Line 61:
 
*vertebrata  
 
*vertebrata  
 
and many more. Run the following command to see all available species:
 
and many more. Run the following command to see all available species:
  $ ls /ufrc/data/reference/busco/
+
  $ ls /data/reference/busco/
  
 
Example of busco run with metazoa dataset:
 
Example of busco run with metazoa dataset:

Revision as of 19:19, 11 February 2021

Description

busco website  

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

Required Modules

Serial

  • busco

System Variables

  • HPC_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/config.ini
$ export BUSCO_CONFIG_FILE=/home/username/config.ini
$ run_BUSCO.py


Datasets are located in /data/reference/busco/


Available datasets:

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

and many more. Run the following command to see all available species:

$ ls /data/reference/busco/

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 an existing Augustus dataset create a local copy of the data and set $AUGUSTUS_CONFIG_PATH variable to that path as explained on the Augustus page.

Example

Let's copy aspergillus_nidulans

mkdir -p augustus/species

  • Load the busco module and copy augustus data
cp $AUGUSTUS_CONFIG_PATH/species/aspergillus_nidulans/ augustus/species/
  • Copy the models
cp $AUGUSTUS_CONFIG_PATH/model augustus/

Add

export AUGUSTUS_CONFIG_PATH=$(pwd)/augustus

to the busco job script and submit it.



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