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    113 repositories

    • 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•18•2•Updated Mar 29, 2025Mar 29, 2025

    • cg

      Public
      Glue between Clinical Genomics apps
      Python
      •3•9•80•27•Updated Mar 28, 2025Mar 28, 2025

    • reference-files

      Public
      Small reference files
      Lua
      •2•5•4•1•Updated Mar 28, 2025Mar 28, 2025

    • cg_lims

      Public
      Python
      •1•3•85•4•Updated Mar 28, 2025Mar 28, 2025

    • scout

      Public
      VCF visualization interface
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •48•162•182•0•Updated Mar 28, 2025Mar 28, 2025

    • BALSAMIC

      Public
      Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
      bioinformaticsgenomicsvariant-callingsomatic-mutationssnakemake-workflows
      Python
      •
      MIT License
      •16•45•91•5•Updated Mar 28, 2025Mar 28, 2025

    • hermes

      Public
      Communication layer between CG and the pipelines.
      Python
      •0•1•4•2•Updated Mar 28, 2025Mar 28, 2025

    • chanjo2

      Public
      Persistent coverage analysis tool using the d4 format
      Python
      •0•2•15•0•Updated Mar 28, 2025Mar 28, 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

    • schug

      Public
      All you need to know about genes, transcripts and exons
      Python
      •0•0•8•1•Updated Mar 25, 2025Mar 25, 2025

    • genmod

      Public
      Annotate models of genetic inheritance patterns in variant files (vcf files)
      Python
      •
      MIT License
      •19•79•20•0•Updated Mar 21, 2025Mar 21, 2025

    • preClinVar

      Public
      A ClinVar API submission helper written in FastAPI
      Python
      •
      MIT License
      •0•1•7•0•Updated Mar 20, 2025Mar 20, 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
      •11•26•3•0•Updated Mar 19, 2025Mar 19, 2025

    • gens

      Public
      JavaScript
      •
      Mozilla Public License 2.0
      •5•1•7•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

    • trailblazer

      Public
      Keep track of and manage analyses
      bioinformaticspython3
      Python
      •
      MIT License
      •2•6•5•2•Updated Mar 11, 2025Mar 11, 2025

    • genotype-api

      Public
      Rewrite of genotype package
      Python
      •1•0•15•1•Updated Mar 11, 2025Mar 11, 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•32•5•1•Updated Mar 4, 2025Mar 4, 2025

    • Janus

      Public
      Repository to collect, parse and ship of multiqc data from housekeeper to cg.
      Python
      •0•0•2•2•Updated Feb 7, 2025Feb 7, 2025

    • snippets

      Public
      Code snippets and one liners
      Shell
      •0•1•0•0•Updated Jan 30, 2025Jan 30, 2025

    • TestRepo_Remove-

      Public archive
      short-read Nono-Invasive Prenatal pipeline evaluation Tool
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

    • udni-tip2toe

      Public
      UDNI tip2toe deep phenotyping frontend
      Java
      •4•1•7•0•Updated Jan 28, 2025Jan 28, 2025

    • ampliseq

      Public
      Amplicon sequencing analysis workflow using DADA2 and QIIME2
      Nextflow
      •
      MIT License
      •130•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • housekeeper

      Public
      File data orchestrator
      datafileorchestrator
      Python
      •
      MIT License
      •0•2•2•0•Updated Jan 27, 2025Jan 27, 2025

    • cg-mockapi

      Public
      Python
      •0•0•0•0•Updated Jan 23, 2025Jan 23, 2025

    • raredisease

      Public
      CG's rare disease pipeline in next flow, see the main repo here 👇
      pipelineanalysisnextflowclinicalvariants
      Nextflow
      •
      MIT License
      •44•5•14•0•Updated Jan 21, 2025Jan 21, 2025

    • MUTANT

      Public
      Microbial Utility Toolbox And wrapper for data traNsmission and Transformation
      Python
      •
      GNU General Public License v3.0
      •1•0•28•2•Updated Jan 21, 2025Jan 21, 2025

    • crunchy

      Public
      Compress fastq files with spring and check the integrity
      Python
      •
      MIT License
      •1•1•2•1•Updated Jan 13, 2025Jan 13, 2025

    • loqusdb

      Public
      A simple observation count database
      Python
      •
      MIT License
      •9•9•17•5•Updated Jan 9, 2025Jan 9, 2025

    • chanjo

      Public
      Chanjo provides a better way to analyze coverage data in clinical sequencing.
      pythoncoveragesqlgenomicsbiocondasambamba
      Python
      •
      MIT License
      •12•50•30•1•Updated Dec 10, 2024Dec 10, 2024