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    57 repositories

    • 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

    • test-datasets

      Public
      Test data to be used for automated testing with the nf-core pipelines
      MIT License
      •496•1•0•0•Updated Apr 14, 2026Apr 14, 2026

    • tronflow-vcf-postprocessing

      Public
      A Nextflow variant normalization pipeline based on vt and bcftools
      bioinformaticsnextflowvcf
      bioinformaticsnextflowvcfvtbcftoolsnormalizing-variantstronflow
      Shell
      •
      MIT License
      •1•6•1•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•9•12•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

    • EasyFuse

      Public
      EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.
      Python
      •
      GNU General Public License v3.0
      •16•66•5•0•Updated Apr 9, 2026Apr 9, 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

    • snakemake

      Public
      This is the development home of the workflow management system Snakemake. For general information, see
      Python
      •
      MIT License
      •634•0•0•0•Updated Mar 16, 2026Mar 16, 2026

    • paneldesign

      Public
      R package to design and evaluate sequencing panels
      R
      •
      Other
      •0•0•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

    • VariantMedium

      Public
      Sensitive and generalizable somatic point mutation calling with 3D DenseNets
      Python
      •
      Other
      •2•2•2•0•Updated Feb 25, 2026Feb 25, 2026

    • snakedeploy

      Public
      deploy a snakemake pipeline directly from version control (under development)
      Python
      •
      Mozilla Public License 2.0
      •13•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•4•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

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.9k•0•0•0•Updated Jan 13, 2026Jan 13, 2026

    • arcasHLA

      Public
      Fast and accurate in silico inference of HLA genotypes from RNA-seq
      Python
      •
      GNU General Public License v3.0
      •58•1•1•0•Updated Dec 14, 2025Dec 14, 2025

    • splice2neo

      Public
      R package to analyze aberrant splicing junctions in tumor samples to identify neoepitopes
      R
      •
      Other
      •2•14•1•0•Updated Nov 25, 2025Nov 25, 2025

    • 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
      •16•0•0•0•Updated Oct 15, 2025Oct 15, 2025

    • mkGCPct

      Public
      Scripts to make GC% RDA files for FACETS
      Shell
      •1•0•0•0•Updated Oct 14, 2025Oct 14, 2025

    • mhcquant

      Public
      Identify and quantify MHC eluted peptides from mass spectrometry raw data
      Nextflow
      •
      MIT License
      •34•0•0•0•Updated Sep 18, 2025Sep 18, 2025

    • snakemake-wrappers

      Public
      This is the development home of the Snakemake wrapper repository, see
      Python
      •210•0•0•0•Updated Sep 17, 2025Sep 17, 2025

    • DEEPctMUT

      Public
      Tumor-naïve ctDNA mutation detection pipeline
      Python
      •
      MIT License
      •0•1•2•0•Updated Sep 12, 2025Sep 12, 2025

    • seq2HLA

      Public
      In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a …
      Python
      •
      MIT License
      •9•51•15•2•Updated Aug 9, 2025Aug 9, 2025

    • tronmake-modules

      Public
      A set of well defined SnakeMake modules for integration into pipelines.
      MIT License
      •0•0•0•0•Updated Jun 25, 2025Jun 25, 2025

    • bam2tensor

      Public
      Toolbox for generating tensors from BAM files
      Python
      •
      MIT License
      •0•1•0•0•Updated Apr 23, 2025Apr 23, 2025

    • testp

      Public
      0•0•0•0•Updated Mar 14, 2025Mar 14, 2025

    • test

      Public
      Test project
      0•0•1•0•Updated Mar 6, 2025Mar 6, 2025

    • easyquant

      Public
      Quantification of reads at defined positions to verify custom input sequences.
      Python
      •
      MIT License
      •0•4•3•0•Updated Mar 5, 2025Mar 5, 2025
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