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    72 repositories

    • bonsai

      Public
      Visualize and analyze resistance and outbreak of bacterial pathogen
      Python
      •
      GNU General Public License v3.0
      •3•8•39•8•Updated Aug 11, 2026Aug 11, 2026

    • SomaticPanelPipeline

      Public
      Nextflow
      •2•1•28•3•Updated Aug 11, 2026Aug 11, 2026

    • virtitta

      Public
      Visualization of virus, designed to work with Virpipa
      Python
      •
      Mozilla Public License 2.0
      •0•0•0•0•Updated Aug 11, 2026Aug 11, 2026

    • coyote3

      Public
      Coyote3 is a secure, scalable, and extensible web application designed as a one-stop solution for genomic variant interpretation, data management, and clinical …
      genomic-data-analysiscoyote3reportingtooling
      genomic-data-analysiscoyote3reportingtooling
      Python
      •
      Other
      •2•0•49•4•Updated Aug 10, 2026Aug 10, 2026

    • cll_genie

      Public
      CLL Genie is a web application for managing LymphoTrack data, IMGT/V-QUEST analysis, IGHV mutation assessment, and clinical CLL reporting.
      Python
      •0•1•4•0•Updated Aug 6, 2026Aug 6, 2026

    • nextflow_tumwgs

      Public
      Perl
      •2•2•16•0•Updated Aug 6, 2026Aug 6, 2026

    • virpipa

      Public
      Virus assembly pipeline. First for HCV
      Nextflow
      •
      Mozilla Public License 2.0
      •0•0•0•0•Updated Jul 31, 2026Jul 31, 2026

    • Pelops

      Public
      Python
      •
      Other
      •4•0•0•0•Updated Jul 29, 2026Jul 29, 2026

    • bonsai-sdk

      Public
      bonsai-libs is the shared Python library for the Bonsai platform. It provides common building blocks used by Bonsai services and tools.
      Python
      •
      GNU General Public License v3.0
      •0•1•0•2•Updated Jul 10, 2026Jul 10, 2026

    • bonsai-prp

      Public
      Pipeline output Processing Program for Bonsai
      Python
      •
      GNU General Public License v3.0
      •2•0•10•2•Updated Jul 9, 2026Jul 9, 2026

    • jasentool

      Public
      Helper tool for all of jasen's needs
      Python
      •
      GNU General Public License v3.0
      •0•0•5•1•Updated Jul 9, 2026Jul 9, 2026

    • PGxModule

      Public
      PGxModule is an advanced Nextflow DSL2 workflow, designed to seamlessly integrate into your genomics pipeline. It empowers you to generate sample-specific repor…
      Nextflow
      •
      GNU General Public License v3.0
      •0•1•7•0•Updated Jul 6, 2026Jul 6, 2026

    • nextflow_wgs

      Public
      Nextflow
      •6•10•121•5•Updated Jul 3, 2026Jul 3, 2026

    • scout

      Public
      VCF visualization interface
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •51•0•0•0•Updated Jun 16, 2026Jun 16, 2026

    • coyote_cli

      Public
      command line interface for coyote
      Python
      •1•0•4•2•Updated Jun 16, 2026Jun 16, 2026

    • nallo

      Public
      An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.
      Nextflow
      •
      MIT License
      •24•0•0•0•Updated Jun 14, 2026Jun 14, 2026

    • PrecisionPGx

      Public
      Nextflow
      •2•1•26•3•Updated Jun 1, 2026Jun 1, 2026

    • nextflow_rnaseqfus

      Public
      Fusion genes identification pipeline
      Nextflow
      •4•1•11•0•Updated May 25, 2026May 25, 2026

    • PipeEval

      Public
      Evaluate changes to your pipelines.
      Python
      •
      Apache License 2.0
      •2•0•12•1•Updated May 11, 2026May 11, 2026

    • smd-variant-tools

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated May 7, 2026May 7, 2026

    • trana

      Public
      A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.
      Nextflow
      •
      GNU General Public License v3.0
      •7•0•0•0•Updated May 5, 2026May 5, 2026

    • haeger

      Public
      Helper for Automated Generation and Execution of Routines
      Python
      •0•0•0•0•Updated Apr 27, 2026Apr 27, 2026

    • gens

      Public
      TypeScript
      •
      Mozilla Public License 2.0
      •9•19•60•1•Updated Apr 24, 2026Apr 24, 2026

    • samplenator-cli

      Public
      Python
      •0•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • jasen

      Public
      Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
      Nextflow
      •
      GNU General Public License v3.0
      •11•0•0•0•Updated Mar 24, 2026Mar 24, 2026

    • eyrie

      Public
      Visualisation software for trana output
      HTML
      •
      MIT License
      •1•4•3•0•Updated Mar 23, 2026Mar 23, 2026

    • genmod

      Public
      Annotate models of genetic inheritance patterns in variant files (vcf files)
      Python
      •
      MIT License
      •22•0•0•0•Updated Mar 18, 2026Mar 18, 2026

    • nextflow_ST_rnaseqfus

      Public
      A rnaseq fussion detection assay at CMD
      Nextflow
      •0•0•1•0•Updated Mar 10, 2026Mar 10, 2026

    • Nisse

      Public
      Post-processing pipeline for Tomte
      Nextflow
      •1•0•5•0•Updated Feb 27, 2026Feb 27, 2026

    • Prepare-Gens-input-data

      Public
      Collection of scripts for preparing input data to Gens (https://github.com/SMD-Bioinformatics-Lund/gens)
      Python
      •
      MIT License
      •0•0•1•0•Updated Feb 26, 2026Feb 26, 2026
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