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

Usage

Load the needed 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

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

Edit the configuration file. The changes required are all in the last portion, which is the only portion shown below:

File : partial_busco_config.ini

[tblastn]
# path to tblastn
path = $EBROOTBLASTPLUS/bin

[makeblastdb]
# path to makeblastdb
path = $EBROOTBLASTPLUS/bin

[augustus]
# path to augustus
path = $EBROOTAUGUSTUS/bin

[etraining]
# path to augustus etraining
path = $EBROOTAUGUSTUS/bin

# path to augustus perl scripts, redeclare it for each new script
[gff2gbSmallDNA.pl]
path = $EBROOTAUGUSTUS/scripts
[new_species.pl]
path = $EBROOTAUGUSTUS/scripts
[optimize_augustus.pl]
path = $EBROOTAUGUSTUS/scripts

[hmmsearch]
# path to HMMsearch executable
path = $EBROOTHMMER/bin

[Rscript]
# path to Rscript, if you wish to use the plot tool
path = $EBROOTR/bin

Check that it runs:

[name@server ~]$ BUSCO_CONFIG_FILE=$HOME/busco_config.ini run_BUSCO.py -v
BUSCO 3.0.2

or

[name@server ~]$ export BUSCO_CONFIG_FILE=$HOME/busco_config.ini
[name@server ~]$ run_BUSCO.py -v
BUSCO 3.0.2