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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 20 2

  5. genomeassembly genomeassembly Public

    Implementation of ToL genome assembly workflows

    Nextflow 20 2

  6. yahs yahs Public

    Forked from c-zhou/yahs

    Yet another Hi-C scaffolding tool

    C 19 4

Repositories

Showing 10 of 49 repositories
  • 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 Dec 9, 2024
  • curationpretext Public

    A Nextflow DSL2 pipeline for pretext generation in curation

    sanger-tol/curationpretext’s past year of commit activity
    Nextflow 6 4 10 1 Updated Dec 9, 2024
  • 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.

    sanger-tol/genomenote’s past year of commit activity
    Python 24 MIT 6 12 (1 issue needs help) 0 Updated Dec 9, 2024
  • variantcalling Public

    Nextflow DSL2 pipeline to call variants on long read alignment.

    sanger-tol/variantcalling’s past year of commit activity
    Nextflow 3 MIT 3 15 (3 issues need help) 0 Updated Dec 9, 2024
  • insdcdownload Public

    Nextflow DSL2 pipeline to download assemblies from INSDC.

    sanger-tol/insdcdownload’s past year of commit activity
    Groovy 1 MIT 2 4 (1 issue needs help) 0 Updated Dec 9, 2024
  • ensemblgenedownload Public

    Nextflow DSL2 pipeline to download gene annotations from Ensembl.

    sanger-tol/ensemblgenedownload’s past year of commit activity
    Groovy 1 MIT 2 3 0 Updated Dec 9, 2024
  • ensemblrepeatdownload Public

    Nextflow DSL2 pipeline to download repeat annotations from Ensembl.

    sanger-tol/ensemblrepeatdownload’s past year of commit activity
    Groovy 1 MIT 1 3 0 Updated Dec 9, 2024
  • sequencecomposition Public

    Nextflow DSL2 pipeline to extract statistics from a genome about its sequence composition

    sanger-tol/sequencecomposition’s past year of commit activity
    Groovy 2 MIT 1 20 (7 issues need help) 1 Updated Dec 9, 2024
  • longreadmag Public
    sanger-tol/longreadmag’s past year of commit activity
    Nextflow 1 MIT 0 0 1 Updated Dec 6, 2024
  • treeval Public

    Pipelines for the production of Treeval data

    sanger-tol/treeval’s past year of commit activity
    Nextflow 23 5 29 (1 issue needs help) 2 Updated Dec 6, 2024
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