Tree of Life pipeline suite

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

Quick reference links

The Tree of Life programme has developed an extensive suite of pipelines that are used in production to assemble reference genomes for projects such as Darwin Tree of Life, and to pre-analyse those genomes to speed-up research.

The workflows are designed with three aims in mind

Biodiversity projects

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

Bioinformaticians and researchers

We write portable, documented and easy to use workflows. Pipelines that just work !

Pipeline developers

The pipelines are modular, reusable & configurable pipelines that follow the nf-core model.

Further information

License and Citation

MIT license

Sanger Institute Contributors

Will Eagles

Senior Bioinformatician

Ksenia Krasheninnikova

Senior Bioinformatician

Dr Matthieu Muffato

Informatics Infrastructure Team Lead

Damon-Lee Pointon

Bioinformatician

Dr Priyanka Surana

BioDev Network Lead

Previous contributors

Dr Ying Yan

Former Senior Bioinformatician at the Sanger Institute

Related groups

Science group

Tree of Life Assembly

Genome Engine

The Assembly team implements the pipelines used to generate reference genome assemblies.

Science group

Tree of Life Informatics Infrastructure

Tree of Life Programme

The Informatics Infrastructure team defines the framework and the implementation guidelines, and develops the analysis pipelines.

External partners and funders

External

Nextflow

Our pipelines are implemented using the Nextflow workflow manager and leverage its latest features (modularity - DSL2 - and containeration).

External

nf-core community

Our pipeline suite relies extensively on tooling and code written by the nf-core community. We contribute back to the community as many modules as we can.

Wellcome Sanger Institute

Programmes and Facilities

Programme

Tree of Life

Investigates the diversity of complex organisms through sequencing and cellular technologies. We generate and use high-quality genome sequences to explore the ...

Collaboration

Darwin Tree of Life Project

The objectives (size and throughput) of the Darwin Tree of Life project have been the determining factor in defining the pipeline ...