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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:

$ module load BUSCO/3.0.2

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

$ run_BUSCO.py -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 3.0.2
$ module load python/3.6.1
$ sudo mkdir /export/apps/BUSCO/3.0.2
$ sudo chown aorth /export/apps/BUSCO/3.0.2
$ python -m venv /export/apps/BUSCO/3.0.2
$ . /export/apps/BUSCO/3.0.2/bin/activate
$ python setup.py install
$ cp -rv * /export/apps/BUSCO/3.0.2
$ cp /export/apps/BUSCO/3.0.2/config/config.ini.default /export/apps/BUSCO/3.0.2/config/config.ini
# edit paths in /export/apps/BUSCO/3.0.2/config/config.ini
$ sudo chown -R root:root /export/apps/BUSCO/3.0.2

Consult the file BUSCO_v3_userguide.pdf for more installation and usage tips.

busco-software.txt · Last modified: 2017/09/11 16:07 by aorth