BUSCO
BUSCO stands for "Benchmarking sets of Universal Single-Copy Orthologs".
It is an application for assessing genome assembly and annotation completeness.
For more information see the user manual.
Available versions
The version 3.0.2 of BUSCO is installed as a module on cvmfs and accessible on all clusters. See below how to use it. For the newer versions, it is possible to install them locally using a virtual environment as follow:
[name@server ~]$ ~ $ module load python/3.7.4
~ $ git clone https://gitlab.com/ezlab/busco.git
~ $ virtualenv /home/$USER/busco_env
~ $ source /home/$USER/busco_env/bin/activate
(busco_env) [~]$ pip install Biopython
(busco_env) [~]$ cd ~/busco
(busco_env) [~]$ python setup.py install
(busco_env) [~]$ cp -r scripts test_data /home/$USER/busco_env/
and add "home/$USER/busco_env/scripts" to your path.
Usage
1. Load the necessary modules:
[name@server ~]$ module load gcc/5.4.0 busco/3.0.2 blast+/2.6.0 hmmer/3.1b2 augustus/3.2.3/ emboss/6.6.0 r/3.5.0
2. Copy the configuration file:
[name@server ~]$ cp -v $EBROOTBUSCO/config/config.ini.default $HOME/busco_config.ini
or
[name@server ~]$ wget -O $HOME/busco_config.ini https://gitlab.com/ezlab/busco/raw/master/config/config.ini.default
3. Edit the configuration file. The locations of external tools are all specified in the last section, which is shown below:
[tblastn]
# path to tblastn
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/blast+/2.6.0/bin
[makeblastdb]
# path to makeblastdb
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/blast+/2.6.0/bin
[augustus]
# path to augustus
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/augustus/3.2.3/bin
[etraining]
# path to augustus etraining
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/augustus/3.2.3/bin
# path to augustus perl scripts, redeclare it for each new script
[gff2gbSmallDNA.pl]
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/augustus/3.2.3/scripts
[new_species.pl]
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/augustus/3.2.3/scripts
[optimize_augustus.pl]
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/augustus/3.2.3/scripts
[hmmsearch]
# path to HMMsearch executable
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/hmmer/3.1b2/bin
[Rscript]
# path to Rscript, if you wish to use the plot tool
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/r/3.5.0/bin
4. Copy the Augustus config directory to a writable location:
[name@server ~]$ cp -r $EBROOTAUGUSTUS/config $HOME/augustus_config
5. Check that it runs:
[name@server ~]$ export BUSCO_CONFIG_FILE=$HOME/busco_config.ini
[name@server ~]$ export AUGUSTUS_CONFIG_PATH=$HOME/augustus_config
[name@server ~]$ run_BUSCO.py --in $EBROOTBUSCO/sample_data/target.fa --out TEST --lineage_path $EBROOTBUSCO/sample_data/example --mode genome
Troubleshooting
Cannot write to Augustus config path
Make sure you have copied the config directory to a writable location and exported the AUGUSTUS_CONFIG_PATH variable.