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@populationgenomics Centre for Population Genomics

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    62 repositories

    • production-pipelines

      Public
      Genomics workflows for CPG using Hail Batch
      genome-analysishailseqrbioinformaticspipeline
      Python
      •
      MIT License
      •1•6•40•38•Updated Oct 31, 2024Oct 31, 2024

    • talos

      Public
      Rare Disease variant reanalysis tool
      Python
      •
      MIT License
      •4•6•11•3•Updated Oct 31, 2024Oct 31, 2024

    • analysis-runner

      Public
      Python
      •
      MIT License
      •4•2•9•7•Updated Oct 31, 2024Oct 31, 2024

    • mocha-wgs

      Public
      A WDL workflow for running MoChA on WGS data
      WDL
      •2•0•0•0•Updated Oct 31, 2024Oct 31, 2024

    • sv-workflows

      Public
      Structural Variation Workflows
      Python
      •
      MIT License
      •1•1•2•8•Updated Oct 30, 2024Oct 30, 2024

    • cpg-flow

      Public
      CPG Pipeline Python API
      Makefile
      •
      MIT License
      •0•0•0•2•Updated Oct 30, 2024Oct 30, 2024

    • metamist

      Public
      Sample level metadata system
      Python
      •
      MIT License
      •1•1•41•23•Updated Oct 30, 2024Oct 30, 2024

    • saige-tenk10k

      Public
      Hail batch pipeline to run SAIGE on CPG's GCP
      Python
      •
      MIT License
      •0•0•5•1•Updated Oct 29, 2024Oct 29, 2024

    • cpg-infrastructure

      Public
      This repository is used to manage the infrastructure at the CPG
      Python
      •
      MIT License
      •1•3•6•4•Updated Oct 25, 2024Oct 25, 2024

    • images

      Public
      Reusable single-software docker images
      Dockerfile
      •
      MIT License
      •1•1•2•8•Updated Oct 25, 2024Oct 25, 2024

    • team-docs

      Public
      Documentation, guides, tips and tricks when working at the CPG
      Python
      •
      MIT License
      •1•1•3•8•Updated Oct 23, 2024Oct 23, 2024

    • hail

      Public
      Scalable genomic data analysis.
      Python
      •
      MIT License
      •246•1•3•1•Updated Oct 23, 2024Oct 23, 2024

    • cpg-utils

      Public
      Library of convenience functions specific to the CPG
      Python
      •
      MIT License
      •1•0•2•2•Updated Oct 22, 2024Oct 22, 2024

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •89•3•31•6•Updated Oct 22, 2024Oct 22, 2024

    • cpg-python-template-repo

      Public template
      A template repository for python code, implementing the CPG setup guidelines
      MIT License
      •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • gnomad-browser

      Public
      Explore gnomAD datasets on the web
      TypeScript
      •
      MIT License
      •43•0•0•0•Updated Oct 11, 2024Oct 11, 2024

    • 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
      •0•1•0•1•Updated Oct 8, 2024Oct 8, 2024

    • renovate-test

      Public
      MIT License
      •0•0•0•1•Updated Oct 4, 2024Oct 4, 2024

    • gnomad_methods

      Public
      Hail helper functions for the gnomAD project and Translational Genomics Group
      Python
      •
      MIT License
      •28•0•0•1•Updated Sep 16, 2024Sep 16, 2024

    • tob-wgs

      Public
      Tasmanian Ophthalmic Biobank Whole Genome Sequencing Project
      Python
      •
      MIT License
      •0•0•1•5•Updated Aug 30, 2024Aug 30, 2024

    • references

      Public
      Reference data for bioinformatics workflows
      Python
      •
      MIT License
      •2•1•2•3•Updated Aug 21, 2024Aug 21, 2024

    • pre-commits

      Public
      Repository of common pre-commit hooks
      Python
      •
      MIT License
      •0•0•0•2•Updated Aug 17, 2024Aug 17, 2024

    • variant-curation-portal

      Public
      Web application for curating loss of function variants
      Python
      •
      MIT License
      •1•1•4•0•Updated Jul 31, 2024Jul 31, 2024

    • cromwell-kccg-mutect2-chip

      Public
      Detect clonal haematopoiesis of indeterminate potential (CHIP) mutations using the GATK4 Mutect2 somatic variant calling pipeline and the Cromwell workflow engine.
      WDL
      •3•0•0•0•Updated Jul 19, 2024Jul 19, 2024

    • sgs-somatic-mutation

      Public
      Genomic Medicine Lab repository for somatic variant analysis
      Python
      •
      MIT License
      •2•0•0•0•Updated Jun 24, 2024Jun 24, 2024

    • exome-results-browsers

      Public
      Results browsers for case-control studies of psychiatric diseases done at the Broad Institute
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •4•0•11•1•Updated Jun 6, 2024Jun 6, 2024

    • cpg-methods

      Public
      Methods developed by the Centre for Population Genomics
      MIT License
      •0•0•0•1•Updated May 29, 2024May 29, 2024

    • ourdna

      Public
      Python
      •
      MIT License
      •0•0•0•1•Updated May 22, 2024May 22, 2024

    • TRTools

      Public
      Toolkit for genome-wide analysis of tandem repeats
      Python
      •
      MIT License
      •20•0•0•0•Updated May 20, 2024May 20, 2024

    • mrff-cnv-reanalysis

      Public
      MIT License
      •0•0•0•0•Updated May 16, 2024May 16, 2024