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. Note: to plot BUSCO summary results, use the companion command: generate_plot.py -wd [WORKING_DIRECTORY] [OTHER OPTIONS] The plotting script is installed as a standalone executable and can be invoked directly as above. DO NOT call it ‘python3 scripts/generate_plot.py’ (as the user manual at https://busco.ezlab.org/busco_userguide.html#plot suggests). This change is specific to the way this container is organized.
Versions
5.4.1
5.4.7
Commands
busco
generate_plot.py
Example job
Warning
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 clusters:
#!/bin/bash
#SBATCH -p PartitionName # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=busco
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module purge
module load busco/XXXX ### you can run *module avail busco* to check all available versions