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    118 repositories

    • cg

      Public
      Glue between Clinical Genomics apps
      Python
      •3•11•121•39•Updated Feb 20, 2026Feb 20, 2026

    • parabellum

      Public
      Paraphase JSON parser
      Python
      •0•0•1•1•Updated Feb 20, 2026Feb 20, 2026

    • oncorefiner

      Public
      Repo for secondary layer of WGS cancer analyses
      Nextflow
      •
      MIT License
      •0•0•5•2•Updated Feb 20, 2026Feb 20, 2026

    • scout

      Public
      VCF visualization interface
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •51•177•224•8•Updated Feb 20, 2026Feb 20, 2026

    • BALSAMIC

      Public
      Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
      bioinformaticsgenomicsvariant-callingsomatic-mutationssnakemake-workflows
      Python
      •
      MIT License
      •15•58•82•10•Updated Feb 19, 2026Feb 19, 2026

    • taxprofiler_metaval_cascade

      Public
      Chaining wrapper between taxprofiler and metaval
      0•0•0•1•Updated Feb 18, 2026Feb 18, 2026

    • reference-files

      Public
      Small reference files
      Lua
      •2•5•9•1•Updated Feb 16, 2026Feb 16, 2026

    • gens

      Public
      JavaScript
      •
      Mozilla Public License 2.0
      •9•1•9•1•Updated Feb 16, 2026Feb 16, 2026

    • microSALT

      Public
      Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.
      pipelinetypingclinicalresistancemicrobial
      Python
      •
      GNU General Public License v3.0
      •3•3•17•1•Updated Feb 16, 2026Feb 16, 2026

    • mutacc-auto

      Public
      Scripts to run mutacc import functionality automatically
      Python
      •0•0•0•0•Updated Feb 10, 2026Feb 10, 2026

    • chanjo

      Public
      Chanjo provides a better way to analyze coverage data in clinical sequencing.
      pythoncoveragesqlgenomicsbiocondasambamba
      Python
      •
      MIT License
      •12•50•31•2•Updated Feb 9, 2026Feb 9, 2026

    • hermes

      Public
      Communication layer between CG and the pipelines.
      Python
      •0•1•6•5•Updated Feb 5, 2026Feb 5, 2026

    • meatballs

      Public
      An open source recipe book from the awesome staff of Clinical Genomics
      Python
      •
      MIT License
      •1•2•4•30•Updated Jan 30, 2026Jan 30, 2026

    • test-datasets

      Public
      Test data to be used for automated testing with the nf-core pipelines
      MIT License
      •461•0•0•0•Updated Jan 28, 2026Jan 28, 2026

    • statina-ui

      Public
      Frontend app for Statina
      TypeScript
      •0•0•1•0•Updated Jan 26, 2026Jan 26, 2026

    • loqusdb

      Public
      A simple observation count database
      Python
      •
      MIT License
      •9•11•19•7•Updated Jan 13, 2026Jan 13, 2026

    • genmod

      Public
      Annotate models of genetic inheritance patterns in variant files (vcf files)
      Python
      •
      MIT License
      •21•85•23•4•Updated Jan 5, 2026Jan 5, 2026

    • genotype-api

      Public
      Rewrite of genotype package
      Python
      •1•0•15•1•Updated Dec 29, 2025Dec 29, 2025

    • trailblazer

      Public
      Keep track of and manage analyses
      bioinformaticspython3
      Python
      •
      MIT License
      •2•6•5•3•Updated Dec 18, 2025Dec 18, 2025

    • stranger

      Public
      Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat
      bioinformaticslong-readlong-read-sequencingshort-tandem-repeatsmassively-parallel-sequencing
      Python
      •
      MIT License
      •6•39•9•0•Updated Dec 15, 2025Dec 15, 2025

    • raredisease

      Public
      CG's rare disease pipeline in next flow, see the main repo here 👇
      pipelineanalysisnextflowclinicalvariants
      Nextflow
      •
      MIT License
      •58•6•14•1•Updated Dec 15, 2025Dec 15, 2025

    • chanjo2

      Public
      Persistent coverage analysis tool using the d4 format
      Python
      •
      MIT License
      •0•3•15•0•Updated Dec 9, 2025Dec 9, 2025

    • schug

      Public
      All you need to know about genes, transcripts and exons
      Python
      •
      MIT License
      •0•0•6•0•Updated Dec 4, 2025Dec 4, 2025

    • MIP

      Public
      Mutation Identification Pipeline. Read the latest documentation:
      pipelineanalysisclinicalvariants
      Perl
      •
      MIT License
      •10•47•11•1•Updated Nov 18, 2025Nov 18, 2025

    • chromograph

      Public
      Genetics graphing tool
      Python
      •
      MIT License
      •3•4•6•1•Updated Nov 14, 2025Nov 14, 2025

    • preClinVar

      Public
      A ClinVar API submission helper written in FastAPI
      Python
      •
      MIT License
      •0•1•8•0•Updated Nov 5, 2025Nov 5, 2025

    • rna-fx

      Public
      nf-core/rnafusion and gms/tomte chaining
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Nov 3, 2025Nov 3, 2025

    • chanjo-report

      Public
      Report generator for Chanjo output
      Python
      •
      MIT License
      •6•0•3•0•Updated Oct 29, 2025Oct 29, 2025

    • loqusdbapi

      Public
      A simple REST api for loqusdb
      Python
      •
      MIT License
      •0•1•11•0•Updated Oct 29, 2025Oct 29, 2025

    • udni-tip2toe

      Public
      UDNI tip2toe deep phenotyping frontend
      Java
      •4•1•5•0•Updated Oct 15, 2025Oct 15, 2025