Skip to content

@broadinstitute Broad Institute

Change the repository type filter

All

    Repositories list

    1.4k repositories

    • fiss-mcp

      Public
      MCP server for Terra
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Nov 8, 2025Nov 8, 2025

    • viral-pipelines

      Public
      viral-ngs: complete pipelines
      WDL
      •
      Other
      •29•67•24•18•Updated Nov 8, 2025Nov 8, 2025

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •22•23•21•8•Updated Nov 7, 2025Nov 7, 2025

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      TypeScript
      •
      BSD 2-Clause "Simplified" License
      •1•8•0•9•Updated Nov 7, 2025Nov 7, 2025

    • viral-core

      Public
      viral-ngs: read QC, barcode metrics, spike-in metrics, Illumina metrics and demux
      Python
      •
      Other
      •1•4•10•2•Updated Nov 7, 2025Nov 7, 2025

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•25•0•4•Updated Nov 7, 2025Nov 7, 2025

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•1•0•Updated Nov 7, 2025Nov 7, 2025

    • long-read-pipelines

      Public
      Long read production pipelines
      pipelineswdlvariant-callingde-novo-assemblylong-reads
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •25•150•95•25•Updated Nov 7, 2025Nov 7, 2025

    • ddp-study-server

      Public
      Pepper Study Server
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •7•8•1•2•Updated Nov 7, 2025Nov 7, 2025

    • sherlock

      Public
      DSP DevOps's deployment source-of-truth service
      golangpostgresgorm
      Go
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•3•Updated Nov 7, 2025Nov 7, 2025

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •75•194•93•32•Updated Nov 7, 2025Nov 7, 2025

    • bmxp

      Public
      The tools that constitute a nontargeted LCMS metabolomics data processing pipeline, created and used by the Broad Institute Metabolomics Platform.
      Python
      •
      Other
      •0•13•0•0•Updated Nov 7, 2025Nov 7, 2025

    • cromwell

      Public
      Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
      dockerapplicationworkflowcloudbioinformaticsscalaexecutorhpccontainerswdl
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •374•1k•757•53•Updated Nov 7, 2025Nov 7, 2025

    • poolq

      Public
      The Genetic Perturbation Platform's tool for deconvoluting and quantifying the results of pooled screens
      Scala
      •
      Other
      •1•5•8•2•Updated Nov 7, 2025Nov 7, 2025

    • depmap-omics-wgs

      Public
      Python
      •0•0•3•0•Updated Nov 7, 2025Nov 7, 2025

    • gnomad_qc

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •28•68•6•10•Updated Nov 7, 2025Nov 7, 2025

    • TRExplorer

      Public
      An online portal for exploring tandem repeats (TRs) genome-wide.
      HTML
      •
      MIT License
      •0•0•5•0•Updated Nov 7, 2025Nov 7, 2025

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticssparkgenomicsgenomengssequencingdnagatk
      Java
      •
      Other
      •619•1.9k•1.3k•144•Updated Nov 7, 2025Nov 7, 2025

    • gnomad_chets

      Public
      Phase of compound heterozygotes in gnomAD
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•6•2•3•Updated Nov 7, 2025Nov 7, 2025

    • bican-mccarroll-manuscript1

      Public
      Scripts used to process data for the first McCarroll lab BICAN manuscript
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 7, 2025Nov 7, 2025

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •90•195•53•4•Updated Nov 7, 2025Nov 7, 2025

    • seqr-helm

      Public
      Helm charts for the seqr project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•5•1•Updated Nov 7, 2025Nov 7, 2025

    • gumbo_client

      Public
      python client for DepMap Gumbo database
      Python
      •0•5•1•0•Updated Nov 7, 2025Nov 7, 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 Nov 7, 2025Nov 7, 2025

    • mad4hatter_wdls

      Public
      Repo for conversion of mad4hatter pipelines
      WDL
      •0•0•0•1•Updated Nov 7, 2025Nov 7, 2025

    • depmap-omics-long-read-rna

      Public
      Python
      •0•2•0•0•Updated Nov 7, 2025Nov 7, 2025

    • nf-pooled-cellpainting-assets

      Public
      Python
      •2•0•0•0•Updated Nov 7, 2025Nov 7, 2025

    • gnomad_methods

      Public
      Hail helper functions for the gnomAD project and Translational Genomics Group
      genomicsgenomesexomeshail
      Python
      •
      MIT License
      •31•97•9•9•Updated Nov 7, 2025Nov 7, 2025

    • orsp-pub

      Public
      Public ORSP Compliance Portal
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•25•Updated Nov 7, 2025Nov 7, 2025

    • warp

      Public
      Warp Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •111•217•6•9•Updated Nov 7, 2025Nov 7, 2025