BUSCO v1.0

BUSCO (Benchmarking Universal Single-Copy Orthologs) is used for assessing genome assembly and annotation completeness.

Accessing the software

To load the module:

$ module load apps/busco/v1.0

An example command to include in your job script:

python $BUSCO_ROOT/BUSCO_v1.0.py -o NAME -in ASSEMBLY -l LINEAGE -m genome

Where:

  • NAME is the name to use for the run and all temporary files.
  • ASSEMBLY is the genome assembly file in fasta format.
  • LINEAGE is the one-letter code for the BUSCO lineage data to use (M,E,A,V,F,B).

If a job requires access to the standard profiles they must first be accessible from the directory that the job is running in; the easiest way to achieve this is create a symbolic link to the standard profiles in the analysis directory. This can be done by adding the following line to your job script before the python call:

ln -s $BUSCO_PROFILES busco_profiles 2>/dev/null

Now, in the python call you can set LINEAGE to busco_profiles/anthropoda to use the standard profile for anthropoda.

The BUSCO modules also sets some extra environment variables for convenience:

  • BUSCO_SAMPLES refers to the samples directory provided with BUSCO.
  • BUSCO_PROFILES contains the profiles downloaded from http://busco.ezlab.org.
  • BUSCO_ASSESSMENTS contains the assessments downloaded from http://busco.ezlab.org.

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations

None.

Other Information

The Support Level for this application is An.

Visit the BUSCO website for more information regarding this application.


Last modified: 13 October 2017