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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 27 7

  2. genomenote genomenote Public

    This Nextflow DSL2 pipeline takes aligned HiC reads, creates contact maps and a table of statistics.

    Groovy 23 6

  3. treeval treeval Public

    Pipelines for the production of Treeval data

    Nextflow 22 3

  4. PretextMap PretextMap Public

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

    C 20 2

  5. yahs yahs Public

    Forked from c-zhou/yahs

    Yet another Hi-C scaffolding tool

    C 19 3

  6. genomeassembly genomeassembly Public

    Implementation of ToL genome assembly workflows

    Nextflow 19 2

Repositories

Showing 10 of 43 repositories
  • singularity-hpc Public Forked from singularityhub/singularity-hpc

    Local filesystem registry for containers (intended for HPC) using Lmod or Environment Modules. Works for users and admins.

    sanger-tol/singularity-hpc’s past year of commit activity
    Python 0 MPL-2.0 27 1 1 Updated Sep 28, 2024
  • tolid-api Public

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

    sanger-tol/tolid-api’s past year of commit activity
    Python 0 0 0 3 Updated Sep 27, 2024
  • treeval Public

    Pipelines for the production of Treeval data

    sanger-tol/treeval’s past year of commit activity
    Nextflow 22 3 32 (1 issue needs help) 4 Updated Sep 27, 2024
  • blobtoolkit Public

    Nextflow pipeline for BlobToolKit for Sanger ToL production suite

    sanger-tol/blobtoolkit’s past year of commit activity
    Nextflow 11 MIT 1 4 1 Updated Sep 26, 2024
  • pipelines-website Public Forked from nf-core/website

    Code and files for the sanger-tol pipelines website.

    sanger-tol/pipelines-website’s past year of commit activity
    PHP 1 MIT 187 0 11 Updated Sep 26, 2024
  • 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 3 MIT 0 9 0 Updated Sep 26, 2024
  • summary-stats-analyses Public
    sanger-tol/summary-stats-analyses’s past year of commit activity
    Python 0 MIT 1 0 0 Updated Sep 26, 2024
  • 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 8 MIT 6 12 2 Updated Sep 25, 2024
  • 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
    0 MIT 0 0 0 Updated Sep 24, 2024
  • genomeassembly Public

    Implementation of ToL genome assembly workflows

    sanger-tol/genomeassembly’s past year of commit activity
    Nextflow 19 MIT 2 6 2 Updated Sep 23, 2024
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