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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 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 19 4

Repositories

Showing 10 of 49 repositories
  • longreadmag Public
    sanger-tol/longreadmag’s past year of commit activity
    Nextflow 1 MIT 0 0 1 Updated Dec 20, 2024
  • tolqc Public

    ToLQC API and website. This is a mirror of the GitLab repository - please don't commit to this repo.

    sanger-tol/tolqc’s past year of commit activity
    Python 3 1 0 11 Updated Dec 19, 2024
  • treeval Public

    Pipelines for the production of Treeval data

    sanger-tol/treeval’s past year of commit activity
    Nextflow 23 5 26 (1 issue needs help) 0 Updated Dec 19, 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) 2 Updated Dec 16, 2024
  • nf-core-tools Public Forked from nf-core/tools

    Python package with helper tools for the nf-core community.

    sanger-tol/nf-core-tools’s past year of commit activity
    Python 0 MIT 192 2 0 Updated Dec 16, 2024
  • 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 16 (3 issues need help) 1 Updated Dec 16, 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 16, 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 4 0 Updated Dec 16, 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 16, 2024
  • blobtoolkit Public

    Nextflow DSL2 pipeline to generate data for a BlobToolKit analysis. This workflow is part of the Tree of Life production suite.

    sanger-tol/blobtoolkit’s past year of commit activity
    Nextflow 11 MIT 4 7 1 Updated Dec 16, 2024
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