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    65 repositories

    • oblx

      Public
      Reproducible generation of references and resources for next generation sequencing pipelines.
      workflowsnakemakereproducible-research
      workflowsnakemakereproducible-researchngs-analysissnakemake-workflowoblx
      Python
      •
      MIT License
      •0•5•38•6•Updated Aug 11, 2026Aug 11, 2026

    • EasyFuse

      Public
      EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.
      Python
      •16•69•5•0•Updated Aug 10, 2026Aug 10, 2026

    • test-datasets

      Public
      Test data to be used for automated testing with the nf-core pipelines
      MIT License
      •528•1•0•0•Updated Aug 10, 2026Aug 10, 2026

    • snakemake-workflow-catalog

      Public
      A statically generated catalog of available Snakemake workflows
      Python
      •
      MIT License
      •12•0•0•0•Updated Aug 10, 2026Aug 10, 2026

    • snakemake-wrappers

      Public
      This is the development home of the Snakemake wrapper repository, see
      Python
      •213•0•0•0•Updated Jul 27, 2026Jul 27, 2026

    • DEEPctMUT

      Public
      Tumor-naïve ctDNA mutation detection pipeline
      Python
      •
      MIT License
      •0•2•2•0•Updated Jul 27, 2026Jul 27, 2026

    • SpecHLA

      Public
      SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, …
      C++
      •
      MIT License
      •17•0•0•1•Updated Jul 24, 2026Jul 24, 2026

    • VariantMedium

      Public
      Sensitive and generalizable somatic point mutation calling with 3D DenseNets
      Python
      •
      Other
      •2•4•2•0•Updated Jul 13, 2026Jul 13, 2026

    • k4neo

      Public
      k4neo enables easy screening of target sequences against a sequence database generated from a set of defined control samples. This packages handles index genera…
      Python
      •
      Other
      •0•1•15•0•Updated Jul 13, 2026Jul 13, 2026

    • tronmake-kmer-pipeline

      Public
      A Snakemake workflow to build and query large scale k-mer datastructures
      workflowsnakemakek-mer
      workflowsnakemakek-mer
      Python
      •
      MIT License
      •0•3•13•0•Updated Jul 6, 2026Jul 6, 2026

    • k4neo-index-data

      Public
      k4neo sequence database of healthy and tumor tissue transcriptomes.
      Shell
      •
      Other
      •0•0•2•0•Updated Jul 3, 2026Jul 3, 2026

    • qualibam

      Public
      A Nextflow pipeline built in nf-core style for comprehensive BAM file quality control, supporting both DNA and RNA sequencing input. Integrates RustQC, RNA-SeQC…
      Nextflow
      •
      MIT License
      •2•5•9•0•Updated Jul 2, 2026Jul 2, 2026

    • neorasp

      Public
      NEOantigens from RNa-SPlicing
      rna-seqsnakemakesplicing-derived-neoepitopes
      rna-seqsnakemakesplicing-derived-neoepitopes
      Python
      •
      MIT License
      •0•2•0•0•Updated Jul 2, 2026Jul 2, 2026

    • splice2neo

      Public
      R package to analyze aberrant splicing junctions in tumor samples to identify neoepitopes
      R
      •
      Other
      •2•15•2•0•Updated Jun 10, 2026Jun 10, 2026

    • qcpanda

      Public
      TRON-Bioinformatics/qcpanda is a Nextflow (DSL2) pipeline that runs a comprehensive battery of QC tools — SeqKit, FastQC, Sequali, fastp, SortMeRNA, FastQ Scree…
      Nextflow
      •
      MIT License
      •0•3•1•0•Updated Jun 5, 2026Jun 5, 2026

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •4k•0•0•0•Updated May 29, 2026May 29, 2026

    • snakemake

      Public
      This is the development home of the workflow management system Snakemake. For general information, see
      Python
      •
      MIT License
      •653•0•0•0•Updated May 26, 2026May 26, 2026

    • tronflow-bam-preprocessing

      Public
      Nextflow pipeline for the preprocessing of BAM files based on GATK best practices. Marking duplicates, realignment around indels, base quality score recalibrati…
      picardbioinformaticsnextflow
      picardbioinformaticsnextflowgatktronflow
      Nextflow
      •
      MIT License
      •0•5•4•1•Updated Apr 15, 2026Apr 15, 2026

    • tronflow-strelka2

      Public
      Strelka2 nextflow pipeline
      bioinformaticsgenomicsngs
      bioinformaticsgenomicsngsvariant-calling
      Nextflow
      •
      MIT License
      •0•1•0•0•Updated Apr 15, 2026Apr 15, 2026

    • tronflow-vcf-postprocessing

      Public
      A Nextflow variant normalization pipeline based on vt and bcftools
      bioinformaticsnextflowvcf
      bioinformaticsnextflowvcfvtbcftoolsnormalizing-variantstronflow
      Shell
      •
      MIT License
      •1•6•3•0•Updated Apr 14, 2026Apr 14, 2026

    • vafator

      Public
      Annotate variants in a VCF file with technical annotations from one or more BAMs
      bioinformaticsannotationvcf
      bioinformaticsannotationvcfbam
      Jupyter Notebook
      •
      MIT License
      •0•10•16•0•Updated Apr 10, 2026Apr 10, 2026

    • tronflow-alignment

      Public
      Nextflow pipeline for BWA, BWA2 and STAR alignments
      bioinformaticsrna-seqngs
      bioinformaticsrna-seqngsbwatronflow
      Nextflow
      •
      MIT License
      •3•12•0•2•Updated Apr 10, 2026Apr 10, 2026

    • snakemake-executor-plugin-cluster-generic

      Public
      Generic cluster executor for Snakemake
      Python
      •
      MIT License
      •11•0•0•0•Updated Mar 16, 2026Mar 16, 2026

    • paneldesign

      Public
      R package to design and evaluate sequencing panels
      R
      •
      Other
      •0•1•5•1•Updated Mar 16, 2026Mar 16, 2026

    • snakemake-plugin-catalog

      Public
      An automatically updated catalog of Snakemake plugins and their documentation
      Python
      •
      MIT License
      •10•0•0•0•Updated Mar 12, 2026Mar 12, 2026

    • snakedeploy

      Public
      deploy a snakemake pipeline directly from version control (under development)
      Python
      •
      Mozilla Public License 2.0
      •14•0•0•0•Updated Feb 22, 2026Feb 22, 2026

    • configs

      Public
      Repository to store config files for pipelines at TRON
      MIT License
      •0•1•0•0•Updated Jan 27, 2026Jan 27, 2026

    • neofox

      Public
      Annotation of mutated peptide sequences with published or novel potential neoantigen descriptors
      bioinformaticsimmunogenomicsimmunogenicity-prediction
      bioinformaticsimmunogenomicsimmunogenicity-predictioncancer-immunologynetmhciipannetmhcpanneoantigen-annotationneoantigens
      Python
      •
      GNU General Public License v3.0
      •6•34•5•1•Updated Jan 27, 2026Jan 27, 2026

    • tronflow-copy-number-calling

      Public
      A nextflow workflow for copy number calling
      bioinformaticscnv
      bioinformaticscnv
      Nextflow
      •
      MIT License
      •1•1•2•2•Updated Jan 14, 2026Jan 14, 2026

    • arcasHLA

      Public
      Fast and accurate in silico inference of HLA genotypes from RNA-seq
      Python
      •
      GNU General Public License v3.0
      •57•1•2•0•Updated Dec 14, 2025Dec 14, 2025
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