Sanger Tree of Life
The Tree of Life Programme uses DNA sequencing and cellular technologies to investigate the diversity and origins of life on Earth. Our research covers all eukaryotic organisms, which means all complex life with a nucleus in their cells – that is every animal, plant, fungi and protist on the planet.
We use Nextflow and are building our own pipelines following the nf-core methodology. All our pipelines are on GitHub, https://github.com/sanger-tol, and are then listed and documented at https://pipelines.tol.sanger.ac.uk/ which is automatically updated every time a new version is released. Our standard procedure is to deposit the releases on Zenodo (https://zenodo.org/communities/sanger-tol) where they acquire a DOI. In parallel, we manually upload certain versions here, on WorkflowHub.
Web page: https://www.sanger.ac.uk/programme/tree-of-life/
Funding details: Related items
https://orcid.org/0009-0006-9956-0404
Informatics Infrastructure Team Lead, Sanger Institute, Tree of Life programme. Formerly Ensembl Compara, TreeFam, and eHive at EMBL-EBI.
Teams: Tree of Life Genome Assembly, Tree of Life Genome Analysis
Organizations: Wellcome Sanger Institute
We develop a suite of analysis pipelines that will run on every genome produced in Tree of Life, providing a central database of core results available for all.
Space: Sanger Tree of Life
Public web page: Not specified
We gather the high throughput sequence data as it is generated, run quality control analysis to make sure the data is good quality and from the expected species. We assemble the long read sequence data into long contiguous pieces, then use further long-range sequencing data to scaffold the data into chromosome scale blocks. We then manually curate the assembly and submit it to INSDC.
We also develop automated tools and pipelines to enable the high throughput required for ever growing number of ...
Space: Sanger Tree of Life
Public web page: Not specified
Type: Nextflow
Creators: Damon-Lee Pointon, Will Eagles, Ying Sims, Matthieu Muffato, Priyanka Surana
Submitter: Matthieu Muffato
