A simple and scalable Nextflow pipeline to compute genome or transcriptome quality metrics using minibusco. This pipeline is designed for high-throughput assessments of genome assemblies and outputs BUSCO metrics as well as a MultiQC report.
- Parallel BUSCO analysis using
minibusco - Support for multiple genome files via CSV input
- Generates standardized BUSCO summary files
- Optionally includes a MultiQC report
- Compatible with SLURM HPC clusters (e.g., Kütral, Leftraru)
- Singularity support for containerized reproducibility
git clone https://github.com/digenoma-lab/minbusco-nf.git
cd minbusco-nfEnsure you have:
Nextflowinstalledminibuscoinstalled or available in your environment/module- (optional)
multiqcinstalled for report generation - Singularity module (if using cluster profiles)
You must provide a CSV file with a header and a column named path, where each row is the full path to a genome or transcriptome file:
path
/path/to/genome1.fasta
/path/to/genome2.fastaThe path to the BUSCO lineage directory (e.g., mollusca_odb10).
| Parameter | Description | Default |
|---|---|---|
--genomes |
CSV file with genome paths (required) | - |
--busco_lineage |
Lineage dataset name (e.g., mollusca_odb10) |
mollusca_odb10 |
--buscodb |
Path to lineage datasets folder | mb_downloads |
--busco_mode |
BUSCO mode (genome, transcriptome, proteins) |
genome |
--outdir |
Output directory for results | busco_results |
--debug |
Enable dry-run mode with fake outputs | false |
nextflow run busco_genomes.nf \
--genomes genomes.csv \
--busco_lineage mollusca_odb10 \
--buscodb /path/to/mb_downloads \
--outdir results \
-profile kutralThe pipeline includes predefined profiles for:
kutral– UOH HPC cluster with Singularity and SLURMleftraru– NLHPC cluster configuration
Use -profile kutral or -profile leftraru to enable them.
For each genome:
busco_results/
├── genome1/
│ ├── mollusca_odb10/
│ ├── full_table_busco_format.tsv
│ ├── summary.txt
│ └── short_summary_genome1.txt
├── genome2/
│ └── ...
└── multiqc/
└── busco_multiqc_report.html
Additionally:
pipeline_info/folder contains timeline, trace, and DAG reports.
- The pipeline supports a
--debugmode that simulates execution with placeholder files (for testing). minibuscomust be accessible in the environment or container.- The lineage folder (e.g.,
mollusca_odb10) should be downloaded or mounted before execution.
Alex Di Genova – @adigenova
Di Genoma Lab – Universidad de O’Higgins
MIT License.