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    21 repositories

    • workflow-smk-ont-basecalling-correction

      Public
      Workflow for the basecalling and error correction of ONT data.
      MIT License
      •0•0•0•0•Updated Aug 19, 2025Aug 19, 2025

    • template-snakemake

      Public
      Workflow template for Snakemake
      Python
      •
      MIT License
      •1•0•8•0•Updated Aug 13, 2025Aug 13, 2025

    • cubi-tools

      Public
      Python
      •
      MIT License
      •0•1•6•1•Updated Aug 13, 2025Aug 13, 2025

    • template-metadata-files

      Public
      Collection of metadata files (gitignore, pyproject, editorconfig, license etc.) to be used for initializing workflow and project repositories
      MIT License
      •0•0•1•0•Updated Aug 5, 2025Aug 5, 2025

    • .github

      Public
      The CUBI public GitHub profile
      TeX
      •0•1•0•0•Updated Aug 5, 2025Aug 5, 2025

    • workflow-smk-sequence-annotation

      Public
      Snakemake workflow to annotate genomic sequences
      MIT License
      •0•0•0•0•Updated Jul 10, 2025Jul 10, 2025

    • workflow-smk-longread-variant-calling

      Public
      Snakemake workflow for genome variant calling using long reads
      MIT License
      •0•1•0•0•Updated Jun 5, 2025Jun 5, 2025

    • workflow-smk-genome-hybrid-assembly

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Feb 12, 2025Feb 12, 2025

    • workflow-smk-assembly-evaluation

      Public
      Workflow for (vertebrate) assembly evaluation
      MIT License
      •0•0•3•0•Updated Feb 12, 2025Feb 12, 2025

    • project-run-hgsvc-hybrid-assemblies

      Public
      Project repository for the HGSVC phase 3 paper
      Shell
      •
      MIT License
      •0•0•0•0•Updated Feb 12, 2025Feb 12, 2025

    • knowledge-base

      Public
      The CUBI's public knowledge base: a Wiki for how-to instructions, best practices and helpful hints
      MIT License
      •0•2•0•0•Updated Jan 17, 2025Jan 17, 2025

    • workflow-smk-genome-onesie-assembly

      Public
      Snakemake workflow to create genome assemblies using only a single long-read sequencing technology (no hybrid assembly)
      MIT License
      •0•0•0•0•Updated Jan 16, 2025Jan 16, 2025

    • workflow-smk-vcf-annotation

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 15, 2024Dec 15, 2024

    • workflow-smk-build-kmer-db

      Public
      Workflow to build sequence k-mer databases with common tools.
      MIT License
      •0•0•0•0•Updated Sep 3, 2024Sep 3, 2024

    • git-playground

      Public
      Testing repository for messing with git
      0•0•0•0•Updated Apr 19, 2024Apr 19, 2024

    • project-dev-WGS-nfcore-raredisease

      Public
      Lua
      •
      MIT License
      •0•0•0•0•Updated Aug 18, 2023Aug 18, 2023

    • reference-container

      Public
      Build repository for reference container
      Python
      •
      MIT License
      •0•0•4•0•Updated May 5, 2023May 5, 2023

    • TcellExTRECT

      Public
      Fork of Bentham TcellExTRECT tool.
      R
      •
      Other
      •21•0•0•0•Updated Apr 28, 2023Apr 28, 2023

    • bioheads

      Public
      BioHEADS
      0•0•0•0•Updated Mar 22, 2023Mar 22, 2023

    • service-catalog

      Public
      0•0•0•0•Updated Mar 19, 2023Mar 19, 2023

    • workflow-smk-varlociraptor-variant-calling

      Public
      A forked Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
      Python
      •
      MIT License
      •42•0•0•0•Updated Mar 14, 2023Mar 14, 2023