Introduction

sanger-tol/busco is a bioinformatics pipeline to run BUSCO across many genomes and many lineages.

It simply iterates over all requested combinations of genomes and lineages and run BUSCO.

[!WARNING] This pipeline is still in development. Documentation is still missing. To run the pipeline, refer to the test profile and adjust to your own data.

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.

Now, you can run the pipeline using:

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

[!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

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.