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    93 repositories

    • cpg-infrastructure

      Public
      This repository is used to manage the infrastructure at the CPG
      Python
      •
      MIT License
      •1•4•5•5•Updated Dec 11, 2025Dec 11, 2025

    • hail

      Public
      Scalable genomic data analysis.
      Python
      •
      MIT License
      •256•1•3•3•Updated Dec 11, 2025Dec 11, 2025

    • gnomad-browser

      Public
      Explore gnomAD datasets on the web
      TypeScript
      •
      MIT License
      •49•0•0•5•Updated Dec 11, 2025Dec 11, 2025

    • talos

      Public
      Rare Disease variant reanalysis tool
      cpg-flow-pipeline
      Python
      •
      MIT License
      •11•24•12•5•Updated Dec 11, 2025Dec 11, 2025

    • talos_af

      Public
      A Talos-like tool for identifying ACMG Actionable Findings in large cohorts
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 10, 2025Dec 10, 2025

    • metamist

      Public
      Sample level metadata system
      Python
      •
      MIT License
      •2•3•40•28•Updated Dec 10, 2025Dec 10, 2025

    • production-pipelines

      Public
      Genomics workflows for CPG using Hail Batch
      bioinformaticspipelinegenome-analysishailseqr
      Python
      •
      MIT License
      •2•10•48•42•Updated Dec 10, 2025Dec 10, 2025

    • team-docs

      Public
      Documentation, guides, tips and tricks when working at the CPG
      Python
      •
      MIT License
      •1•3•3•8•Updated Dec 10, 2025Dec 10, 2025

    • cpg-flow

      Public
      CPG Pipeline Python API
      Python
      •
      MIT License
      •0•0•7•9•Updated Dec 10, 2025Dec 10, 2025

    • cpg-flow-rdrnaseq

      Public
      Python
      •
      MIT License
      •0•0•0•1•Updated Dec 10, 2025Dec 10, 2025

    • cpg-flow-stripy

      Public
      workflowbioinformaticspipelinecpgcpg-flow-pipeline
      HTML
      •
      MIT License
      •0•0•1•0•Updated Dec 10, 2025Dec 10, 2025

    • cpg-flow-seqr-loader

      Public
      workflowbioinformaticspipelinecpgcpg-flow-pipeline
      Python
      •
      MIT License
      •0•0•0•3•Updated Dec 10, 2025Dec 10, 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 Dec 10, 2025Dec 10, 2025

    • images

      Public
      Reusable single-software docker images
      Dockerfile
      •
      MIT License
      •2•1•1•10•Updated Dec 9, 2025Dec 9, 2025

    • talos_manuscript

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•1•Updated Dec 9, 2025Dec 9, 2025

    • dragen_align_rd

      Public
      ICA communication workflow, to trigger and retrieve DRAGEN analyses. RD team edition
      0•0•0•0•Updated Dec 8, 2025Dec 8, 2025

    • cpg-utils

      Public
      Library of convenience functions specific to the CPG
      Python
      •
      MIT License
      •1•0•2•1•Updated Dec 5, 2025Dec 5, 2025

    • analysis-runner

      Public
      Python
      •
      MIT License
      •5•2•7•6•Updated Dec 5, 2025Dec 5, 2025

    • cpg-flow-mito

      Public
      workflowbioinformaticspipelinecpgcpg-flow-pipeline
      Python
      •
      MIT License
      •0•0•0•1•Updated Dec 4, 2025Dec 4, 2025

    • cpg-flow-align-genotype

      Public
      cpg-flow-pipeline
      Python
      •
      MIT License
      •0•0•4•0•Updated Dec 4, 2025Dec 4, 2025

    • tgg-terraform-modules

      Public
      HCL
      •3•0•0•0•Updated Dec 4, 2025Dec 4, 2025

    • cpg-flow-gatk-sv

      Public
      CPG-Flow implementation of the GATK-SV pipeline, deployed at the Centre for Population Genomics
      workflowbioinformaticspipelinecpgcpg-flow-pipeline
      Python
      •
      MIT License
      •0•0•2•2•Updated Dec 4, 2025Dec 4, 2025

    • dragen_align_pa

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 4, 2025Dec 4, 2025

    • seqr-helm

      Public
      Helm charts for the seqr project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•0•0•Updated Dec 3, 2025Dec 3, 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
      •3•5•2•0•Updated Dec 3, 2025Dec 3, 2025

    • ourdna-browser

      Public
      Makefile
      •
      MIT License
      •0•1•0•1•Updated Dec 3, 2025Dec 3, 2025

    • single_sample_qc_popgen

      Public
      Single Sample QC Pipeline for the Population Genomics Team at CPG
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 1, 2025Dec 1, 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 Nov 5, 2025Nov 5, 2025

    • ica-sdk-python

      Public
      Python
      •0•0•0•0•Updated Nov 3, 2025Nov 3, 2025

    • flowa

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 26, 2025Oct 26, 2025