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@sanger-tol

Tree of Life programme

The Tree of Life Programme investigates the diversity of complex organisms (eukaryotes) through sequencing and cellular technology
README.md

Hello 👋 !

You can find here most of the production code used by the Tree of Life 🌍 programme at the Sanger Institute, including the suite of Nextflow pipelines ⚙️ we use to generate hundreds of high-quality reference genome assemblies.

We also use these organisations and repositories:

Visit our main website at https://pipelines.tol.sanger.ac.uk/ to learn more about our mission 🧑‍🚀 !

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  1. PretextView PretextView Public

    OpenGL Powered Pretext Contact Map Viewer

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  2. treeval treeval Public

    Pipelines for the production of Treeval data

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  3. genomenote genomenote Public

    Nextflow DSL2 pipeline to generate a Genome Note, including assembly statistics, quality metrics, and Hi-C contact maps. This workflow is part of the Tree of Life production suite.

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  4. genomeassembly genomeassembly Public

    Implementation of ToL genome assembly workflows

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  5. PretextMap PretextMap Public

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Repositories

Showing 10 of 66 repositories
  • genomeassembly Public

    Implementation of ToL genome assembly workflows

    sanger-tol/genomeassembly’s past year of commit activity
    Nextflow 25 MIT 6 5 2 Updated Jan 23, 2026
  • components Public

    UI components - this is a mirror of the internal GitLab repository. Please do not commit to this repo.

    sanger-tol/components’s past year of commit activity
    TypeScript 0 0 0 0 Updated Jan 23, 2026
  • tol-sdk Public

    The Tree of Life Python SDK. This is a mirror of the GitLab repository - please don't commit to this repo.

    sanger-tol/tol-sdk’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Jan 23, 2026
  • hifi-trimmer Public
    sanger-tol/hifi-trimmer’s past year of commit activity
    Python 4 MIT 0 1 0 Updated Jan 23, 2026
  • tol-submissions Public

    ToL Submissions service. This is a mirror of the GitLab repository - please don't commit to this repo.

    sanger-tol/tol-submissions’s past year of commit activity
    Python 0 0 0 3 Updated Jan 22, 2026
  • PretextMap Public

    Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.

    sanger-tol/PretextMap’s past year of commit activity
    C 24 4 5 0 Updated Jan 22, 2026
  • nf-core-modules Public

    Repository to host Tree of Life's Nextflow DSL2 modules

    sanger-tol/nf-core-modules’s past year of commit activity
    Nextflow 0 MIT 1 8 1 Updated Jan 22, 2026
  • tola-data Public

    Data management for the Tree of Life genome assembly pipeline

    sanger-tol/tola-data’s past year of commit activity
    Python 1 MIT 1 0 0 Updated Jan 21, 2026
  • readmapping Public

    Nextflow DSL2 pipeline to align short and long reads to genome assembly. This workflow is part of the Tree of Life production suite.

    sanger-tol/readmapping’s past year of commit activity
    Nextflow 13 MIT 8 22 (3 issues need help) 1 Updated Jan 21, 2026
  • ascc Public

    A Nextflow DSL2 pipeline for the identification of cobiont and contaminating sequences using fasta and pacbio data.

    sanger-tol/ascc’s past year of commit activity
    Python 6 MIT 3 27 5 Updated Jan 21, 2026
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