End-to-end suite of pipelines, from genome assembly to genome analysis.
Portable, documented and easy to use workflows.
Pipelines that just work.
Modular, reusable & configurable pipelines that follow the nf-core model.
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.
Extensive documentation covering installation, usage and description of output files makes sanger-tol pipelines easy to run.
Every time a change is made to the pipeline code, sanger-tol pipelines use continuous-integration testing to ensure that nothing has broken.
sanger-tol pipelines use GitHub and Zenodo releases to tag stable versions of the code and software, making pipeline runs totally reproducible.
Pipeline dependencies are automatically downloaded and handled using Docker, Singularity, Conda or others. No need for any software installations.
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 Seqera Platform before release.
All pipelines and modules must be based on nf-core templates and be created using nf-core tools.
Research teams from the Sanger and partner institutes helped define the scope and content of each pipeline.
Scale and diversity in Tree of Life make the pipelines exceptionally well tested and suitable for a wide range of organisms (eukaryotes).
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.
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
Check out the available pipelines to see if we have what you need. Each comes with release details, keywords and a description.
Available pipelinesRead 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 TutorialIf you're interested in contributing to sanger-tol, take a look at the developer documentation to see what's required.
Developer docs
