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@icgc-argo-workflows ICGC ARGO Workflows

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    42 repositories

    • metadata-for-benchmarking-datasets

      Public
      This repository contains metadata information for PCAWG WGS/RNA-Seq/Validation datasets
      Python
      •2•1•0•0•Updated Mar 26, 2026Mar 26, 2026

    • vcfqc

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 25, 2025Sep 25, 2025

    • dnaalnqc

      Public
      ICGC-ARGO workflow for DNA-Seq alignment QC
      mupad
      •
      MIT License
      •1•4•0•0•Updated Sep 25, 2025Sep 25, 2025

    • xml_variant_ingestion

      Public
      ICGC ARGO variant calling pipeline which digest xml to vcf variant format
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Jul 10, 2025Jul 10, 2025

    • target_seq_bed_files

      Public
      A repository to capture genes targeted by WES and target-Seq from ICGC-ARGO projects
      MIT License
      •0•0•0•0•Updated Jun 26, 2025Jun 26, 2025

    • prealnqc

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated May 26, 2025May 26, 2025

    • argo-modules

      Public
      ARGO specific modules using nf-core framework
      HTML
      •
      MIT License
      •0•0•3•1•Updated Apr 25, 2025Apr 25, 2025

    • icgc-argo-mutational-signatures

      Public
      ICGC ARGO Mutational Signatures Workflow Packages
      Nextflow
      •
      MIT License
      •0•3•0•0•Updated Oct 28, 2024Oct 28, 2024

    • vcf-annotation

      Public
      ICGC ARGO Workflow for VCF Annotation
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Oct 17, 2024Oct 17, 2024

    • rnaaln

      Public
      ICGC ARGO Workflow for RNA-Seq Alignment
      GNU Affero General Public License v3.0
      •0•0•0•1•Updated Sep 23, 2024Sep 23, 2024

    • dnaaln

      Public
      ICGC ARGO Workflow for DNA-Seq Alignment
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Aug 20, 2024Aug 20, 2024

    • dna-seq-processing-wfs

      Public
      ICGC ARGO DNA-Seq Processing Workflow
      workflowbioinformaticsnextflow
      workflowbioinformaticsnextflowcancer-genomicsdna-seq
      Nextflow
      •
      GNU Affero General Public License v3.0
      •4•5•2•0•Updated Jul 23, 2024Jul 23, 2024

    • argo-reference-files

      Public
      Reference files used by the ICGC-ARGO data analysis pipelines
      GNU Affero General Public License v3.0
      •0•0•1•0•Updated Jul 3, 2024Jul 3, 2024

    • rna-seq-alignment

      Public
      RNA-Seq alignment packages
      Nextflow
      •
      MIT License
      •1•5•0•0•Updated Apr 18, 2024Apr 18, 2024

    • sanger-wgs-variant-calling

      Public
      ICGC-ARGO Sanger WGS Somatic Variant Calling Workflow
      workflowbioinformaticsgenomics
      workflowbioinformaticsgenomicscancer
      Nextflow
      •
      GNU Affero General Public License v3.0
      •3•4•3•0•Updated Mar 26, 2024Mar 26, 2024

    • rna-seq-expression-counting

      Public
      Nextflow
      •
      MIT License
      •0•1•0•0•Updated Jan 2, 2024Jan 2, 2024

    • germlinevar

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jun 30, 2023Jun 30, 2023

    • open-access-variant-filtering

      Public
      Nextflow
      •
      GNU Affero General Public License v3.0
      •1•1•0•0•Updated Jun 29, 2023Jun 29, 2023

    • gatk-mutect2-variant-calling

      Public
      ICGC ARGO GATK Mutect2 Somatic Variant Calling Workflow
      workflowbioinformaticsgenomics
      workflowbioinformaticsgenomicscancer
      Nextflow
      •
      GNU Affero General Public License v3.0
      •2•0•1•0•Updated Jun 29, 2023Jun 29, 2023

    • sanger-wxs-variant-calling

      Public
      ICGC-ARGO Sanger WXS Somatic Variant Calling Workflow
      workflowbioinformaticsgenomics
      workflowbioinformaticsgenomicscancer
      Nextflow
      •
      GNU Affero General Public License v3.0
      •1•0•0•0•Updated Jun 29, 2023Jun 29, 2023

    • data-processing-utility-tools

      Public
      Collection of utility tools for ARGO data processing
      Python
      •
      GNU Affero General Public License v3.0
      •2•0•0•0•Updated Jun 8, 2023Jun 8, 2023

    • nextflow-data-processing-utility-tools

      Public
      Nextflow implementation of https://github.com/icgc-argo/data-processing-utility-tools
      Nextflow
      •
      Apache License 2.0
      •1•0•2•0•Updated May 30, 2023May 30, 2023

    • ase

      Public
      ICGC-ARGO pipeline for analysis of allele specific expression (ASE) based on RNA-seq data
      0•0•0•0•Updated May 2, 2023May 2, 2023

    • pre-alignment-qc

      Public
      Python
      •
      GNU Affero General Public License v3.0
      •1•0•0•0•Updated Mar 9, 2023Mar 9, 2023

    • rna-seq-data-simulation

      Public
      Data simulation scripts for RNA-Seq working group
      Python
      •0•0•0•0•Updated Nov 3, 2022Nov 3, 2022

    • allele-specific-expression

      Public
      Allele Specific Expression (ASE) analysis package
      Python
      •
      MIT License
      •1•6•0•0•Updated Aug 16, 2022Aug 16, 2022

    • argo-qc-tools

      Public
      Collection of ARGO data quality tool packages
      HTML
      •
      MIT License
      •1•1•0•0•Updated Jun 28, 2022Jun 28, 2022

    • dna-seq-processing-tools

      Public
      A collection of DNA processing tools / modules used in the ICGC ARGO alignment workflow
      workflowbioinformaticsgenomics
      workflowbioinformaticsgenomicscancer
      Python
      •
      GNU Affero General Public License v3.0
      •1•3•1•0•Updated Jun 23, 2022Jun 23, 2022

    • gatk-rna-mutect2-variant-calling

      Public
      GATK Variant Calling for RNA-Seq
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated May 26, 2022May 26, 2022

    • argo-analysis-pipelines-overview

      Public
      Overview of ICGC-ARGO Analysis Pipelines
      GNU Affero General Public License v3.0
      •0•1•0•0•Updated May 18, 2022May 18, 2022
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