busco-software
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Table of Contents
BUSCO
BUSCO (Benchmarking Universal Single-Copy Orthologs) assesses genome assembly and annotation completeness with single-copy ortholog.
Information
- Latest Version: 4.0.6
- Added: August, 2015
- Updated: May, 2020
- Link: https://busco.ezlab.org
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
See the BUSCO documentation for more information about how to use it: https://busco.ezlab.org/busco_userguide.html#running-busco
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.1640691195.txt.gz · Last modified: 2021/12/28 11:33 by aorth