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    114 repositories

    • BALSAMIC

      Public
      Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
      bioinformaticsgenomicsvariant-callingsomatic-mutationssnakemake-workflows
      Python
      •
      MIT License
      •15•49•109•16•Updated Aug 1, 2025Aug 1, 2025

    • cg

      Public
      Glue between Clinical Genomics apps
      Python
      •3•9•66•29•Updated Aug 1, 2025Aug 1, 2025

    • 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•2•17•2•Updated Jul 28, 2025Jul 28, 2025

    • scout

      Public
      VCF visualization interface
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •50•169•184•9•Updated Jul 25, 2025Jul 25, 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•33•7•1•Updated Jul 25, 2025Jul 25, 2025

    • patientMatcher

      Public
      A MatchMaker Exchange server
      genevariantsmatchmakerscorematchmakingdiagnosissimilarity-scorehpo-similaritypatientsomim
      Python
      •
      MIT License
      •6•11•4•0•Updated Jul 24, 2025Jul 24, 2025

    • hermes

      Public
      Communication layer between CG and the pipelines.
      Python
      •0•1•4•3•Updated Jul 23, 2025Jul 23, 2025

    • schug

      Public
      All you need to know about genes, transcripts and exons
      Python
      •0•0•6•1•Updated Jul 18, 2025Jul 18, 2025

    • chanjo2

      Public
      Persistent coverage analysis tool using the d4 format
      Python
      •0•2•13•0•Updated Jul 17, 2025Jul 17, 2025

    • Scout-REViewer-service

      Public
      A rest service for generating REViewer output.
      Python
      •0•0•9•1•Updated Jul 11, 2025Jul 11, 2025

    • genmod

      Public
      Annotate models of genetic inheritance patterns in variant files (vcf files)
      Python
      •
      MIT License
      •21•82•19•3•Updated Jul 4, 2025Jul 4, 2025

    • genotype

      Public
      Simple genotype comparison of VCF files
      Python
      •
      MIT License
      •2•8•8•5•Updated Jul 3, 2025Jul 3, 2025

    • reference-files

      Public
      Small reference files
      Lua
      •2•5•5•1•Updated Jun 30, 2025Jun 30, 2025

    • loqusdb

      Public
      A simple observation count database
      Python
      •
      MIT License
      •9•11•18•3•Updated Jun 19, 2025Jun 19, 2025

    • fusion-report

      Public
      Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.github.io/fusion-report/example/
      visualizationreportfusion-genes
      Python
      •
      GNU General Public License v3.0
      •12•27•3•0•Updated Jun 13, 2025Jun 13, 2025

    • raredisease

      Public
      CG's rare disease pipeline in next flow, see the main repo here 👇
      pipelineanalysisnextflowclinicalvariants
      Nextflow
      •
      MIT License
      •48•5•12•0•Updated Jun 11, 2025Jun 11, 2025

    • meatballs

      Public
      An open source recipe book from the awesome staff of Clinical Genomics
      Python
      •
      MIT License
      •1•2•3•27•Updated Jun 9, 2025Jun 9, 2025

    • rna-fx

      Public
      nf-core/rnafusion and gms/tomte chaining
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated May 15, 2025May 15, 2025

    • fluffy

      Public
      FetaL AneUploidy and FetalFraction analYsis Pipeline
      Python
      •9•4•0•0•Updated May 8, 2025May 8, 2025

    • cg-deployment

      Public
      Clinical Genomics software deployment API
      Python
      •
      MIT License
      •1•0•2•1•Updated May 6, 2025May 6, 2025

    • salty-reporter

      Public
      A tool to convert JASEN analysis result files in JSON format to the same format as the microSALT reports. Initially used to figure out discrepancies between the tools.
      HTML
      •
      GNU General Public License v3.0
      •0•1•6•0•Updated Apr 30, 2025Apr 30, 2025

    • housekeeper

      Public
      File data orchestrator
      datafileorchestrator
      Python
      •
      MIT License
      •0•2•2•0•Updated Apr 29, 2025Apr 29, 2025

    • arnold

      Public
      Python
      •
      MIT License
      •1•0•4•0•Updated Apr 29, 2025Apr 29, 2025

    • statina

      Public
      Python
      •3•2•20•0•Updated Apr 29, 2025Apr 29, 2025

    • Janus

      Public
      Repository to collect, parse and ship of multiqc data from housekeeper to cg.
      Python
      •0•0•2•2•Updated Apr 28, 2025Apr 28, 2025

    • assets

      Public
      A repo which contains assets such as images
      0•0•0•0•Updated Apr 24, 2025Apr 24, 2025

    • preClinVar

      Public
      A ClinVar API submission helper written in FastAPI
      Python
      •
      MIT License
      •0•1•7•0•Updated Apr 7, 2025Apr 7, 2025

    • snippet_dev

      Public
      short-read Non-Invasive Prenatal pipeline examination Tool
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Mar 26, 2025Mar 26, 2025

    • gens

      Public
      JavaScript
      •
      Mozilla Public License 2.0
      •6•1•8•3•Updated Mar 19, 2025Mar 19, 2025

    • chanjo-report

      Public
      Report generator for Chanjo output
      Python
      •
      MIT License
      •6•0•7•0•Updated Mar 13, 2025Mar 13, 2025