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@populationgenomics Centre for Population Genomics

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    122 repositories

    • cpg-infrastructure

      Public
      This repository is used to manage the infrastructure at the CPG
      Python
      •
      MIT License
      •1•6•4•7•Updated Sep 16, 2026Sep 16, 2026

    • cpg-flow-relatedness

      Public
      Central workflow for all cross-omic QC workflows
      cpg-flow-pipeline
      cpg-flow-pipeline
      Python
      •
      MIT License
      •0•0•0•2•Updated Sep 16, 2026Sep 16, 2026

    • themis

      Public
      Themis — agentic rare-disease curation platform
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 15, 2026Sep 15, 2026

    • sv-workflows

      Public
      Structural Variation Workflows
      Python
      •
      MIT License
      •1•2•2•4•Updated Sep 15, 2026Sep 15, 2026

    • popgen-genotyping

      Public
      A pipeline to process genotyping microarray data using CPG Flow
      Python
      •
      MIT License
      •0•0•2•1•Updated Sep 15, 2026Sep 15, 2026

    • hail

      Public
      Scalable genomic data analysis.
      Python
      •
      MIT License
      •265•1•3•2•Updated Sep 15, 2026Sep 15, 2026

    • references

      Public
      Reference data for bioinformatics workflows
      Python
      •
      MIT License
      •2•2•4•3•Updated Sep 15, 2026Sep 15, 2026

    • analysis-runner

      Public
      Python
      •
      MIT License
      •5•2•7•7•Updated Sep 15, 2026Sep 15, 2026

    • cpg-flow

      Public
      CPG Pipeline Python API
      Python
      •
      MIT License
      •0•0•7•8•Updated Sep 15, 2026Sep 15, 2026

    • seqera-trial-tmp

      Public
      Python
      •0•0•0•0•Updated Sep 14, 2026Sep 14, 2026

    • grus

      Public
      Pedigree IR (protobuf) + deterministic Bennett-standard SVG renderer + importers (PED, kinship2, Phenopackets, Open Pedigree)
      pythonsvgbioinformatics
      pythonsvgbioinformaticsprotobufgeneticspedigree
      Python
      •
      MIT License
      •0•0•0•1•Updated Sep 14, 2026Sep 14, 2026

    • cpg-flow-rdrnaseq

      Public
      Python
      •
      MIT License
      •0•1•0•1•Updated Sep 14, 2026Sep 14, 2026

    • talos2

      Public
      Talos, a tool for clinical variant filtering and automated reanalysis, rewritten without hefty Spark/Hail features
      Python
      •
      MIT License
      •1•3•0•1•Updated Sep 14, 2026Sep 14, 2026

    • cpg-flow-lrs-annotation

      Public
      For creating annotated callsets for seqr from long-read-sequencing data
      Python
      •
      MIT License
      •0•0•2•2•Updated Sep 14, 2026Sep 14, 2026

    • palit

      Public
      PanelApp Australia Literature Assessment
      Python
      •
      MIT License
      •0•0•0•11•Updated Sep 11, 2026Sep 11, 2026

    • images

      Public
      Reusable single-software docker images
      Dockerfile
      •
      MIT License
      •2•1•1•16•Updated Sep 11, 2026Sep 11, 2026

    • talos

      Public
      Rare Disease variant reanalysis tool
      cpg-flow-pipeline
      cpg-flow-pipeline
      Python
      •
      MIT License
      •22•83•8•6•Updated Sep 11, 2026Sep 11, 2026

    • cpg-flow-gatk-sv

      Public
      CPG-Flow implementation of the GATK-SV pipeline, deployed at the Centre for Population Genomics
      workflowbioinformaticspipeline
      workflowbioinformaticspipelinecpgcpg-flow-pipeline
      Python
      •
      MIT License
      •0•0•2•2•Updated Sep 11, 2026Sep 11, 2026

    • 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•11•0•1•Updated Sep 11, 2026Sep 11, 2026

    • flowa

      Public
      TypeScript
      •
      MIT License
      •0•0•0•12•Updated Sep 10, 2026Sep 10, 2026

    • metamist

      Public
      Sample level metadata system
      Python
      •
      MIT License
      •2•3•43•38•Updated Sep 10, 2026Sep 10, 2026

    • rare-disease

      Public
      A collection of scripts relating to rare-disease specific projects
      Python
      •
      MIT License
      •1•2•0•2•Updated Sep 9, 2026Sep 9, 2026

    • cpg-flow-mito

      Public
      workflowbioinformaticspipeline
      workflowbioinformaticspipelinecpgcpg-flow-pipeline
      Python
      •
      MIT License
      •0•0•0•2•Updated Sep 9, 2026Sep 9, 2026

    • cpg-flow-seqr-loader

      Public
      workflowbioinformaticspipeline
      workflowbioinformaticspipelinecpgcpg-flow-pipeline
      Python
      •
      MIT License
      •0•0•1•8•Updated Sep 9, 2026Sep 9, 2026

    • litdown

      Public
      Convert JATS XML articles (PubMed Central format) to Markdown with embedded LaTeX math, for downstream LLM tooling.
      Python
      •
      MIT License
      •1•0•0•0•Updated Sep 8, 2026Sep 8, 2026

    • production-pipelines

      Public
      Genomics workflows for CPG using Hail Batch
      bioinformaticspipelinegenome-analysis
      bioinformaticspipelinegenome-analysishailseqr
      Python
      •
      MIT License
      •2•12•48•37•Updated Sep 8, 2026Sep 8, 2026

    • semantic-code-review

      Public
      LLM-augmented local-diff and GitHub-PR reviewer with foldable semantic diffs and round-trip inline comments.
      Python
      •
      MIT License
      •1•0•0•0•Updated Sep 8, 2026Sep 8, 2026

    • popgen_rbceq2

      Public
      CPG's Population Genomics team repo to implement the rbceq2 pipeline via Nextflow
      Python
      •0•0•0•3•Updated Sep 7, 2026Sep 7, 2026

    • dragen_align_pa

      Public
      Python
      •
      MIT License
      •0•0•0•1•Updated Sep 3, 2026Sep 3, 2026

    • litfetch

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 2, 2026Sep 2, 2026
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