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    85 repositories

    • talos

      Public
      Rare Disease variant reanalysis tool
      Python
      •
      MIT License
      •10•22•11•5•Updated Aug 21, 2025Aug 21, 2025

    • cpg-flow-seqr-loader

      Public
      Python
      •
      MIT License
      •0•0•0•3•Updated Aug 21, 2025Aug 21, 2025

    • cpg-flow-gatk-sv

      Public
      CPG-Flow implementation of the GATK-SV pipeline, deployed at the Centre for Population Genomics
      Python
      •
      MIT License
      •0•0•2•2•Updated Aug 21, 2025Aug 21, 2025

    • pa-sandbox

      Public
      A place to prototype all sorts of disconnected stages and pipelines we want to test out.
      Python
      •
      MIT License
      •0•0•0•1•Updated Aug 21, 2025Aug 21, 2025

    • cpg-infrastructure

      Public
      This repository is used to manage the infrastructure at the CPG
      Python
      •
      MIT License
      •1•4•5•6•Updated Aug 21, 2025Aug 21, 2025

    • metamist

      Public
      Sample level metadata system
      Python
      •
      MIT License
      •2•3•41•29•Updated Aug 20, 2025Aug 20, 2025

    • gnomad-deployments

      Public
      kustomizations for current gnomad project kubernetes deployments
      Makefile
      •1•0•0•0•Updated Aug 20, 2025Aug 20, 2025

    • ourdna-browser

      Public
      Makefile
      •
      MIT License
      •0•0•0•0•Updated Aug 20, 2025Aug 20, 2025

    • cpg-flow

      Public
      CPG Pipeline Python API
      Python
      •
      MIT License
      •0•0•5•5•Updated Aug 15, 2025Aug 15, 2025

    • test_workflows_shared

      Public template
      Python
      •
      MIT License
      •0•0•1•3•Updated Aug 14, 2025Aug 14, 2025

    • gnomad-browser

      Public
      Explore gnomAD datasets on the web
      TypeScript
      •
      MIT License
      •50•0•0•3•Updated Aug 13, 2025Aug 13, 2025

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •90•3•28•3•Updated Aug 13, 2025Aug 13, 2025

    • ourdna-browser-blog

      Public
      JavaScript
      •0•0•0•0•Updated Aug 13, 2025Aug 13, 2025

    • cpg-utils

      Public
      Library of convenience functions specific to the CPG
      Python
      •
      MIT License
      •1•0•2•1•Updated Aug 13, 2025Aug 13, 2025

    • talos_manuscript

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•1•Updated Aug 13, 2025Aug 13, 2025

    • production-pipelines

      Public
      Genomics workflows for CPG using Hail Batch
      genome-analysishailseqrbioinformaticspipeline
      Python
      •
      MIT License
      •1•9•48•42•Updated Aug 12, 2025Aug 12, 2025

    • ClinvArbitration

      Public
      A side-project from the AIP, containing the code, logic, and documentation for the ClinVar consequence reassessment process in use at the CPG
      Python
      •
      MIT License
      •1•5•2•0•Updated Aug 12, 2025Aug 12, 2025

    • sv-workflows

      Public
      Structural Variation Workflows
      Python
      •
      MIT License
      •1•1•2•20•Updated Aug 11, 2025Aug 11, 2025

    • saige-tenk10k

      Public
      Hail batch pipeline to run SAIGE on CPG's GCP
      Python
      •
      MIT License
      •1•4•5•5•Updated Aug 8, 2025Aug 8, 2025

    • cpg-flow-align-genotype

      Public
      Python
      •
      MIT License
      •0•0•5•0•Updated Aug 7, 2025Aug 7, 2025

    • references

      Public
      Reference data for bioinformatics workflows
      Python
      •
      MIT License
      •2•1•4•3•Updated Aug 7, 2025Aug 7, 2025

    • images

      Public
      Reusable single-software docker images
      Dockerfile
      •
      MIT License
      •2•1•1•12•Updated Aug 6, 2025Aug 6, 2025

    • gatk-sv

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •77•0•0•1•Updated Aug 3, 2025Aug 3, 2025

    • healthfutures-evagg

      Public
      Python
      •
      MIT License
      •5•0•0•0•Updated Jul 28, 2025Jul 28, 2025

    • analysis-runner

      Public
      Python
      •
      MIT License
      •5•2•7•5•Updated Jul 23, 2025Jul 23, 2025

    • rare-disease

      Public
      A collection of scripts relating to rare-disease specific projects
      Python
      •
      MIT License
      •1•2•0•1•Updated Jul 21, 2025Jul 21, 2025

    • cpg-flow-lrs-annotation

      Public
      For creating annotated callsets for seqr from long-read-sequencing data
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 21, 2025Jul 21, 2025

    • hail

      Public
      Scalable genomic data analysis.
      Python
      •
      MIT License
      •253•1•3•3•Updated Jul 15, 2025Jul 15, 2025

    • team-docs

      Public
      Documentation, guides, tips and tricks when working at the CPG
      Python
      •
      MIT License
      •1•3•3•7•Updated Jul 11, 2025Jul 11, 2025

    • cpg-flow-pipeline-template

      Public template
      A template repository to use as a base for CPG workflows using the cpg-flow pipeline framework
      Python
      •
      MIT License
      •0•0•0•1•Updated Jul 7, 2025Jul 7, 2025