BUSCO
BUSCO (Benchmarking Universal Single-Copy Orthologs) assesses the completeness of genome assemblies, gene sets and transcriptomes by searching for a set of orthologs that are expected to be present as single-copy genes in a given lineage.
License
Free to use and open source under the MIT License.
Available
- Roihu-CPU: 5.4.3, 6.1.0, via the
bio-appsmodule.
Usage
BUSCO is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the BUSCO module:
BUSCO is run with the busco command, specifying the input, the mode
(genome, proteins or transcriptome) and a lineage dataset:
busco --offline --download_path $BUSCO_DB -i genome.fa -m genome -l eukaryota_odb12.2 -o result -c 8
Lineage datasets
CSC provides all BUSCO lineage datasets on Roihu: odb10 for BUSCO 5.4.3 (for example
eukaryota_odb10) and odb12.2, the default for BUSCO 6.1.0 (for example
eukaryota_odb12.2). The busco module sets
the BUSCO_DB environment variable to their location. Use them with
--offline --download_path $BUSCO_DB, as in the example above.
Always add --offline
The shared lineage directory is read-only. Without --offline, BUSCO tries to
update files in it and the run fails.
Augustus gene predictor
If you run BUSCO with the Augustus gene predictor (--augustus), Augustus needs a
writable configuration directory, because it writes trained species parameters
there. The module provides a snapshot of this configuration via the $CONFIG_TEMPLATE
environment variable. Unpack it to a writable location and point
AUGUSTUS_CONFIG_PATH at it before running BUSCO:
tar -xzf $CONFIG_TEMPLATE -C /scratch/<project>/
export AUGUSTUS_CONFIG_PATH=/scratch/<project>/config
The default gene predictor (Metaeuk/Miniprot) does not require this step.
Example batch script
#!/bin/bash
#SBATCH --job-name=busco
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=08:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4G
module load bio-apps/v202603
module load busco/6.1.0
busco --offline --download_path $BUSCO_DB \
-i genome.fa -m genome -l eukaryota_odb12.2 -o result -c $SLURM_CPUS_PER_TASK
Replace <project> with your CSC project (for example project_2001234).
See creating a batch job script for Roihu for more information about running batch jobs.