Tree of Life pipeline suite

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

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

MIT license

Sanger Institute Contributors

Photo of Will Eagles

Will Eagles

Senior Bioinformatician

Photo of Ksenia Krasheninnikova

Ksenia Krasheninnikova

Senior Bioinformatician

Photo of Dr Matthieu Muffato

Dr Matthieu Muffato

Informatics Infrastructure Team Lead

Photo of Damon-Lee Pointon

Damon-Lee Pointon


Photo of Dr Priyanka Surana

Dr Priyanka Surana

BioDev Network Lead

Previous contributors

Photo of Dr Ying Yan

Dr Ying Yan

Former Senior Bioinformatician at the Sanger Institute

External partners and funders



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


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.