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.

For more information, please check:
Docker hub: https://hub.docker.com/r/ezlabgva/busco
Home page: https://gitlab.com/ezlab/busco/ Note: 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 coniguration 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

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

5.2.2, 5.3.0, 5.4.1, 5.4.3, 5.4.4, 5.4.5, 5.4.7, 5.8.2-py

BELL

5.2.2, 5.3.0, 5.4.1, 5.4.3, 5.4.4, 5.4.5, 5.4.7, 5.8.2-py

GAUTSCHI

5.2.2, 5.3.0, 5.4.1, 5.4.3, 5.4.4, 5.4.5, 5.4.7

NEGISHI

5.2.2, 5.3.0, 5.4.1, 5.4.3, 5.4.4, 5.4.5, 5.4.7, 5.8.2-py

SCHOLAR

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

Module

You can load the modules by:

module load biocontainers
module load busco

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 -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers busco

# Your busco workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers busco

# Your busco workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers busco

# Your busco workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers busco

# Your busco workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers busco

# Your busco workflow...