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    1.4k repositories

    • warp

      Public
      Warp Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •111•215•6•8•Updated Sep 30, 2025Sep 30, 2025

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•25•0•2•Updated Sep 30, 2025Sep 30, 2025

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •90•194•49•4•Updated Sep 30, 2025Sep 30, 2025

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•8•0•8•Updated Sep 30, 2025Sep 30, 2025

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •77•194•88•31•Updated Sep 30, 2025Sep 30, 2025

    • gnomad_qc

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •27•68•6•9•Updated Sep 30, 2025Sep 30, 2025

    • terraform-broad-redirect

      Public
      Terraform configuration for the broad-redirect projects
      HCL
      •0•0•0•1•Updated Sep 30, 2025Sep 30, 2025

    • single_cell_portal_core

      Public
      Rails/Docker application for the Broad Institute's single cell RNA-seq data portal
      rna-seq-analysissingle-cell-genomicshuman-cell-atlas
      Ruby
      •
      BSD 3-Clause "New" or "Revised" License
      •27•68•0•1•Updated Sep 30, 2025Sep 30, 2025

    • long-read-pipelines

      Public
      Long read production pipelines
      pipelineswdlvariant-callingde-novo-assemblylong-reads
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •25•148•95•27•Updated Sep 30, 2025Sep 30, 2025

    • lrma-aou1-panel-creation

      Public
      Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 1 long-reads callset.
      WDL
      •2•1•22•2•Updated Sep 30, 2025Sep 30, 2025

    • CNV-Mag

      Public
      A Tool to Visualize CNV Events in WGS Data
      Python
      •
      MIT License
      •0•2•0•0•Updated Sep 30, 2025Sep 30, 2025

    • gnomad_methods

      Public
      Hail helper functions for the gnomAD project and Translational Genomics Group
      genomicsgenomesexomeshail
      Python
      •
      MIT License
      •30•96•9•9•Updated Sep 30, 2025Sep 30, 2025

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•1•0•Updated Sep 30, 2025Sep 30, 2025

    • poolq

      Public
      The Genetic Perturbation Platform's tool for deconvoluting and quantifying the results of pooled screens
      Scala
      •
      Other
      •1•5•7•3•Updated Sep 30, 2025Sep 30, 2025

    • backstage

      Public
      Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
      TypeScript
      •0•2•0•1•Updated Sep 30, 2025Sep 30, 2025

    • gnomad-browser

      Public
      Explore gnomAD datasets on the web
      javascriptgenomicsgnomad
      TypeScript
      •
      MIT License
      •49•85•165•8•Updated Sep 29, 2025Sep 29, 2025

    • cromwell

      Public
      Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
      dockerapplicationcloudbioinformaticsscalaexecutorhpccontainerswdlga4gh
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •374•1k•757•56•Updated Sep 29, 2025Sep 29, 2025

    • kpt-packages

      Public
      A Catalog of Kpt packages and Blueprints
      MIT License
      •0•1•0•1•Updated Sep 29, 2025Sep 29, 2025

    • dig-aggregator-methods

      Public
      Monorepo of methods implemented for the Aggregator
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•0•8•Updated Sep 29, 2025Sep 29, 2025

    • seqr-helm

      Public
      Helm charts for the seqr project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•3•0•Updated Sep 29, 2025Sep 29, 2025

    • BE3D

      Public
      BE3D public repository
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 29, 2025Sep 29, 2025

    • mad4hatter_wdls

      Public
      Repo for conversion of mad4hatter pipelines
      WDL
      •0•0•0•0•Updated Sep 29, 2025Sep 29, 2025

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •22•23•17•4•Updated Sep 29, 2025Sep 29, 2025

    • depmap-omics-wgs

      Public
      Python
      •0•0•3•0•Updated Sep 29, 2025Sep 29, 2025

    • depmap-omics-long-read-rna

      Public
      Python
      •0•1•0•0•Updated Sep 29, 2025Sep 29, 2025

    • depmap-omics-rna

      Public
      Python
      •0•0•0•0•Updated Sep 29, 2025Sep 29, 2025

    • nebelung

      Public
      Python wrapper for the Firecloud API
      Python
      •0•3•0•0•Updated Sep 29, 2025Sep 29, 2025

    • glama

      Public
      Genomic long-read analysis modules and applications
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•2•Updated Sep 29, 2025Sep 29, 2025

    • jump-profiling-recipe

      Public
      Workflow for processing cpg0016-jump profiles
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•4•9•1•Updated Sep 29, 2025Sep 29, 2025

    • carpenter-singh-lab-guide

      Public
      BSD 3-Clause "New" or "Revised" License
      •0•1•1•1•Updated Sep 29, 2025Sep 29, 2025