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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 🧑‍🚀 !

Popular repositories Loading

  1. PretextView PretextView Public

    OpenGL Powered Pretext Contact Map Viewer

    C 30 8

  2. 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.

    Python 24 6

  3. treeval treeval Public

    Pipelines for the production of Treeval data

    Nextflow 23 5

  4. PretextMap PretextMap Public

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

    C 21 3

  5. genomeassembly genomeassembly Public

    Implementation of ToL genome assembly workflows

    Nextflow 20 3

  6. yahs yahs Public

    Forked from c-zhou/yahs

    Yet another Hi-C scaffolding tool

    C 18 4

Repositories

Showing 10 of 50 repositories
  • variantcalling Public

    Nextflow DSL2 pipeline to call variants on long read alignment.

    sanger-tol/variantcalling’s past year of commit activity
    Nextflow 4 MIT 3 17 (3 issues need help) 0 Updated Jan 22, 2025
  • treeval Public

    Pipelines for the production of Treeval data

    sanger-tol/treeval’s past year of commit activity
    Nextflow 23 5 24 (1 issue needs help) 1 Updated Jan 22, 2025
  • 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
    Nextflow 4 MIT 0 7 1 Updated Jan 22, 2025
  • zippypretext Public

    A pipeline that reuses previously generated Hi-C map data to create a new Hi-C map based on a new assembly structure.

    sanger-tol/zippypretext’s past year of commit activity
    1 MIT 0 0 2 Updated Jan 21, 2025
  • 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 20, 2025
  • rapid-curation Public
    sanger-tol/rapid-curation’s past year of commit activity
    Python 0 MIT 1 0 0 Updated Jan 17, 2025
  • longreadmag Public
    sanger-tol/longreadmag’s past year of commit activity
    Nextflow 1 MIT 0 8 1 Updated Jan 17, 2025
  • variantcomposition Public
    sanger-tol/variantcomposition’s past year of commit activity
    0 1 0 0 Updated Jan 16, 2025
  • ear Public

    ERGA Assembly Report pipeline

    sanger-tol/ear’s past year of commit activity
    Nextflow 0 MIT 0 2 0 Updated Jan 15, 2025
  • 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 11 MIT 6 14 2 Updated Jan 15, 2025
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