Introduction

sanger-tol/busco runs BUSCO on one or many genome assemblies.

The pipeline supports:

• Single-assembly input via --fasta
• Multi-assembly input via --input samplesheet
• Per-assembly lineage selection and/or automated lineage discovery from NCBI taxonomy (taxid)
• Multiple ODB versions in one run via --odb_versions

For each assembly, the pipeline:

1. Decompresses gzipped FASTA files if needed.
2. Selects BUSCO lineage datasets using get_odbs.py and mapping files.
3. Runs BUSCO for every selected lineage.
4. Restructures outputs into a lineage-first layout under busco/.
5. Produces a MultiQC report and standard Nextflow trace files.

Usage

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

Run with a samplesheet:

nextflow run sanger-tol/busco \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
  --odb_versions odb12 \
   --outdir <OUTDIR>

Run with a single FASTA:

nextflow run sanger-tol/busco \
  -profile <docker/singularity/.../institute> \
  --fasta assembly.fasta.gz \
  --taxid 988087 \
  --mode latest \
  --odb_versions odb12 \
  --outdir <OUTDIR>

Required arguments:

• Exactly one input mode: --input or --fasta
• --odb_versions (comma-separated list, e.g. odb10,odb12,odb12.2)
• At least one lineage selection mechanism per sample: mode and/or lineage

If using ancestral or latest mode, taxid is required (global --taxid or per-row samplesheet value).

You can optionally provide --busco_db to run BUSCO in offline mode using local lineage datasets.

For full run instructions, input format, and parameter behavior, see docs/usage.md.

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

sanger-tol/busco was originally written by Tyler Chafin during the Cambridge BioHackathon 2024 with the participation of:

• Pete Dockrill @PeteDockrill
• Axel Rodriguez @errepeAxel

Matthieu Muffato @muffato then updated the pipeline for release under the sanger-tol umbrella organisation.

The pipeline underwent a large reset in v0.2.0 to focus on automating BUSCO runs. Functionality to run the BUSCO steps has been removed but will be reintegrated later.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

If you use sanger-tol/busco for your analysis, please cite:

• 10.5281/zenodo.20275259

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.