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BUSCO

BUSCO (Benchmarking Universal Single-Copy Orthologs) assesses genome assembly and annotation completeness with single-copy ortholog.

Information

Usage

See versions of BUSCO which are available:

$ module avail BUSCO

Load one version into your environment and run it:

$ module load BUSCO/4.0.6

After loading the module, consult the built-in help:

$ busco -h

Note: BUSCO utilizes Augustus and requires you to make a copy of the Augustus configuration for each of your runs as well as set up an environment variable pointing to it, ie:

$ cp -r /export/apps/augustus/3.2.3/config /var/scratch/aorth-augustus-config
$ export AUGUSTUS_CONFIG_PATH=/var/scratch/aorth-augustus-config

Installation

Notes from the sysadmin during installation:

$ cd /tmp
$ git clone https://gitlab.com/ezlab/busco.git
$ cd busco
$ git checkout 4.0.6
$ sudo mkdir /export/apps/BUSCO/4.0.6
$ sudo chown aorth /export/apps/BUSCO/4.0.6
$ python3 -m venv /export/apps/BUSCO/4.0.6
$ source /export/apps/BUSCO/4.0.6/bin/activate
$ pip install --upgrade setuptools pip
$ python setup.py install
$ module load R/3.6
$ mkdir /export/apps/BUSCO/4.0.6/r-libs
$ export R_LIBS=/export/apps/BUSCO/4.0.6/r-libs
$ Rscript -e 'install.packages("ggplot2", repos="https://cran.rstudio.com")'
$ module load blast/2.2.31+ augustus/3.2.3 hmmer/3.2.1 sepp/4.3.8 prodigal/2.6.3
$ ./scripts/busco_configurator.py config/config.ini config/myconfig.ini
$ sudo cp config/myconfig.ini  /export/apps/BUSCO/4.0.6/
$ sudo chown -R root:root /export/apps/BUSCO/4.0.6

Consult the BUSCO user guide for more installation and usage tips.

busco-software.txt · Last modified: 2020/05/12 15:45 by aorth