Workflows and tools to investigate the genomic diversity of complex organisms.

For biodiversity projects

End-to-end suite of pipelines, from genome assembly to genome analysis.

For users

Portable, documented and easy to use workflows.
Pipelines that just work.

For developers

Modular, reusable & configurable pipelines that follow the nf-core model.

PNAS Sequence locally, think globally: The Darwin Tree of Life Project PNAS 119 (4) e2115642118 (2022). PNAS

The Tree of Life production suite is designed to handle nature's diversity.

sanger-tol pipelines use Nextflow DSL2 and adhere to strict nf-core guidelines.

Best-in-class pipelines

Documentation

Extensive documentation covering installation, usage and description of output files makes sanger-tol pipelines easy to run.

CI Testing

Every time a change is made to the pipeline code, sanger-tol pipelines use continuous-integration testing to ensure that nothing has broken.

Stable Releases

sanger-tol pipelines use GitHub and Zenodo releases to tag stable versions of the code and software, making pipeline runs totally reproducible.

Packaged software

Pipeline dependencies are automatically downloaded and handled using Docker, Singularity, Conda or others. No need for any software installations.

Portable and cloud-compatible

Pipelines follow best-practices to ensure maximum portability. You can run the pipelines on any Nextflow supported cloud provider. We test all our pipelines via Nextflow Tower before release.

Made with nf-core

All pipelines and modules must be based on nf-core templates and be created using nf-core tools.

Developed for and with the community

Research teams from the Sanger and partner institutes helped define the scope and content of each pipeline.

Universal

Scale and diversity in Tree of Life make the pipelines exceptionally well tested and suitable for a wide range of organisms (eukaryotes).

Optimised

The high throughput of species in Tree of Life makes us strive for efficiency. We have refined and optimised the resource usage of the sanger-tol pipelines to best utilise compute resources.

Get started in minutes

Nextflow lets you run sanger-tol pipelines on virtually any computing environment.

All sanger-tol pipelines are modifiable with the nf-core tools.

# Install nextflow
curl -s https://get.nextflow.io | bash
mv nextflow ~/bin/

# Launch the readmapping pipeline
nextflow run sanger-tol/readmapping \
    --input samplesheet.csv \
    --fasta genome.fasta \
    -profile singularity

# Install nf-core tools
pip install nf-core

See what's available

Check out the available pipelines to see if we have what you need. Each comes with release details, keywords and a description.

Available pipelines

Run a pipeline

Read the quickstart tutorial to learn how to get set up with the required software and tools, and how to launch a nf-core pipeline.

Quickstart Tutorial

Get into the code

If you're interested in contributing to sanger-tol, take a look at the developer documentation to see what's required.

Developer docs