BUSCO
Description
BUSCO provides quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness, based on evolutionarily-informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB v9.
License
Use
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of busco and load default version of busco as
module avail busco/ # list available modules module load busco # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail busco
and choose explicit version you want to use.
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A newer version of Busco is available via Conda modules
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run_BUSCO.py --help
Please read the documentation for Augustus, Blast+ and HMMER.
You may need to adjust environment variable AUGUSTUS_CONFIG_PATH to point to some writable directory with configurations. Eg.:
mkdir $SCRATCHDIR/augustus_configs cp -r $AUGUSTUS_CONFIG_PATH/* $SCRATCHDIR/augustus_configs/ export AUGUSTUS_CONFIG_PATH=$SCRATCHDIR/augustus_configs
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Datasets (actual to September 2018) are localized in the directory
/software/busco/3.0.2/src/db/ |
Documentation
http://gitlab.com/ezlab/busco/raw/master/BUSCO_v3_userguide.pdf or in directory /software/busco/3.0.2/src.