busco
Link to section 'Introduction' of 'busco' Introduction
BUSCO (Benchmarking sets of Universal Single-Copy Orthologs) provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.
Detailed information can be found here: https://gitlab.com/ezlab/busco/
Link to section 'Versions' of 'busco' Versions
- 5.2.2
- 5.3.0
- 5.4.1
- 5.4.3
- 5.4.4
- 5.4.5
- 5.4.7
Commands
- busco - generate_plot.py
Helper command
Augustus is a gene prediction program for eukaryotes which is required by BUSCO. Augustus requires a writable configuration directory. This installation comes with a stub of AUGUSTUS configuration files, but you must copy them out from the container into a location where you have write permissions.
A helper command copy_augustus_config is provided to simplify the task. Follow the procedure below to put the config files in your scratch space:
$ mkdir -p $RCAC_SCRATCH/augustus
$ copy_augustus_config $RCAC_SCRATCH/augustus
$ export AUGUSTUS_CONFIG_PATH=$RCAC_SCRATCH/augustus/config
Link to section 'Module' of 'busco' Module
You can load the modules by:
module load biocontainers
module load busco
Link to section 'Example job for prokaryotic genomes' of 'busco' Example job for prokaryotic genomes
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run BUSCO on our cluster:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=BUSCO
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers busco
## Print the full lineage datasets, and find the dataset fitting your organism.
busco --list-datasets
## run the evaluation
busco -f -c 12 -l actinobacteria_class_odb10 -i bacteria_genome.fasta -o busco_out -m genome
## generate a simple summary plot
generate_plot.py -wd busco_out
Link to section 'Example job for eukaryotic genomes' of 'busco' Example job for eukaryotic genomes
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run BUSCO on our cluster:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=BUSCO
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers busco
## The augustus config step is only required for the first time to use BUSCO
mkdir -p $RCAC_SCRATCH/augustus
copy_augustus_config $RCAC_SCRATCH/augustus
## This is required for eukaryotic genomes
export AUGUSTUS_CONFIG_PATH=$RCAC_SCRATCH/augustus/config
## Print the full lineage datasets, and find the dataset fitting your organism.
busco --list-datasets
## run the evaluation
busco -f -c 12 -l fungi_odb10 -i fungi_protein.fasta -o busco_out_protein -m protein
busco -f -c 12 --augustus -l fungi_odb10 -i fungi_genome.fasta -o busco_out_genome -m genome
## generate a simple summary plot
generate_plot.py -wd busco_out_protein
generate_plot.py -wd busco_out_genome