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    24 repositories

    • reports

      Public
      Snakemake module for generating reports related to Hydra-Genetics results
      JavaScript
      •
      GNU General Public License v3.0
      •0•1•12•4•Updated Jan 24, 2025Jan 24, 2025

    • references

      Public
      Collection of rules used to create references, panel of normals (PoN), and background filters.
      Python
      •
      GNU General Public License v3.0
      •1•2•12•1•Updated Jan 21, 2025Jan 21, 2025

    • prealignment

      Public
      Snakemake module containing processing steps that should be performed before sequence alignment.
      Python
      •
      GNU General Public License v3.0
      •1•0•1•2•Updated Jan 15, 2025Jan 15, 2025

    • alignment

      Public
      Snakemake module containing processing steps that should be performed during sequence alignment.
      Python
      •
      GNU General Public License v3.0
      •2•3•4•2•Updated Jan 10, 2025Jan 10, 2025

    • filtering

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•6•3•Updated Jan 9, 2025Jan 9, 2025

    • cnv_sv

      Public
      Collection of rules used to call structural variants
      Python
      •
      GNU General Public License v3.0
      •3•3•11•1•Updated Jan 9, 2025Jan 9, 2025

    • biomarker

      Public
      Collection of rules used to calculate biomarkers like MSI, TMB and HRD.
      Python
      •
      GNU General Public License v3.0
      •0•1•6•3•Updated Jan 9, 2025Jan 9, 2025

    • snv_indels

      Public
      Collection of rules used to call snv and small indels.
      Python
      •
      GNU General Public License v3.0
      •2•0•9•2•Updated Jan 9, 2025Jan 9, 2025

    • misc

      Public
      Python
      •
      GNU General Public License v3.0
      •1•0•0•3•Updated Jan 9, 2025Jan 9, 2025

    • fusions

      Public
      fusions
      Python
      •
      GNU General Public License v3.0
      •0•0•6•3•Updated Jan 9, 2025Jan 9, 2025

    • parabricks

      Public
      Snakemake module containing different analyses provided by parabricks.
      Python
      •
      GNU General Public License v3.0
      •1•0•0•1•Updated Jan 9, 2025Jan 9, 2025

    • hydra-genetics

      Public
      Command line interface to create new modules/pipelines or adding a new rule to a existing project. Helper libraries for handling samples and units.
      Python
      •
      GNU General Public License v3.0
      •1•3•12•1•Updated Jan 9, 2025Jan 9, 2025

    • docker

      Public
      Collection of dockerfiles with bioinformatic tools used to execute snakemake with singularity.
      Dockerfile
      •1•2•2•6•Updated Jan 9, 2025Jan 9, 2025

    • annotation

      Public
      Collections of rules to annotate vcf files.
      Python
      •
      GNU General Public License v3.0
      •0•2•6•1•Updated Nov 22, 2024Nov 22, 2024

    • qc

      Public
      Collection of rules performing QC and generating reports.
      Verilog
      •
      GNU General Public License v3.0
      •1•2•14•5•Updated Oct 14, 2024Oct 14, 2024

    • compression

      Public
      Snakemake module containing steps to minimize big files prior to storage
      Python
      •
      GNU General Public License v3.0
      •0•0•0•3•Updated Sep 4, 2024Sep 4, 2024

    • long_read

      Public archive
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 21, 2024Aug 21, 2024

    • mitochondrial

      Public
      Snakemake module for performing Mitochondrial short variant discovery
      Python
      •
      GNU General Public License v3.0
      •0•3•0•2•Updated Jun 17, 2024Jun 17, 2024

    • gitaction-testing

      Public
      Python
      •0•0•0•1•Updated Apr 25, 2024Apr 25, 2024

    • sentieon

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•2•Updated Mar 4, 2024Mar 4, 2024

    • .github

      Public
      Organization information
      GNU General Public License v3.0
      •0•0•0•0•Updated May 22, 2023May 22, 2023

    • multipass

      Public
      0•0•0•0•Updated May 10, 2023May 10, 2023

    • vagrant

      Public
      Vagrant machine used to run snakemake/hydragenetics in combination with singularity on Windows/OSX
      Ruby
      •0•0•0•0•Updated May 10, 2023May 10, 2023

    • profiles

      Public
      Example of configuration profiles for executing Snakemake in various computing environments
      0•0•0•0•Updated Nov 19, 2021Nov 19, 2021