Skip to content

@broadinstitute Broad Institute

Change the repository type filter

All

    Repositories list

    1.4k repositories

    • TAG-public

      Public
      Official workflows published by the Broad Institute's Genomics Platform Translation Analysis Group (TAG)
      WDL
      •3•5•1•15•Updated Feb 6, 2026Feb 6, 2026

    • qprimer_designer

      Public
      Design tool for highly performant qPCR diagnostics.
      Jupyter Notebook
      •
      MIT License
      •1•3•6•2•Updated Feb 6, 2026Feb 6, 2026

    • palantir-workflows

      Public
      Utility workflows for the DSP hydro.gen team (formerly palantir)
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •11•26•4•3•Updated Feb 6, 2026Feb 6, 2026

    • viral-pipelines

      Public
      viral-ngs: complete pipelines
      WDL
      •
      Other
      •30•72•21•20•Updated Feb 6, 2026Feb 6, 2026

    • permutect

      Public
      Permutect, an incredibly efficient deep learning architecture for somatic and germline variant calling
      Python
      •1•8•10•2•Updated Feb 6, 2026Feb 6, 2026

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •93•200•45•6•Updated Feb 6, 2026Feb 6, 2026

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      TypeScript
      •
      BSD 2-Clause "Simplified" License
      •1•8•1•6•Updated Feb 6, 2026Feb 6, 2026

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •76•201•96•26•Updated Feb 6, 2026Feb 6, 2026

    • delphy

      Public
      Fast, scalable, accurate and accessible Bayesian phylogenetics
      C++
      •
      MIT License
      •4•41•0•1•Updated Feb 6, 2026Feb 6, 2026

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticssparkgenomicsgenomengssequencingdnagatk
      Java
      •
      Other
      •622•1.9k•1.3k•143•Updated Feb 6, 2026Feb 6, 2026

    • dig-aggregator-methods

      Public
      Monorepo of methods implemented for the Aggregator
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•1•0•9•Updated Feb 5, 2026Feb 5, 2026

    • warp

      Public
      Warp Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •112•225•6•9•Updated Feb 5, 2026Feb 5, 2026

    • bits-appengine

      Public
      BITS AppEngine Python Package
      Python
      •0•0•0•3•Updated Feb 5, 2026Feb 5, 2026

    • 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
      •377•1.1k•758•50•Updated Feb 5, 2026Feb 5, 2026

    • dsp-appsec-infrastructure-apps

      Public
      This repository hosts DSP AppSec internal infrastructure apps deployed in GKE.
      securityapplication-securityappsecsecurity-scannersecure-developmentsecurity-automationsecurity-toolsdevsecopssecurity-scanappsecurity
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•7•0•11•Updated Feb 5, 2026Feb 5, 2026

    • exome-results-browsers

      Public
      Results browsers for case-control studies of psychiatric diseases done at the Broad Institute
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •4•11•9•8•Updated Feb 5, 2026Feb 5, 2026

    • gnomad_qc

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •29•69•5•13•Updated Feb 5, 2026Feb 5, 2026

    • backstage

      Public
      Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
      TypeScript
      •0•2•0•1•Updated Feb 5, 2026Feb 5, 2026

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •23•23•22•4•Updated Feb 5, 2026Feb 5, 2026

    • depmap_omics

      Public
      What you need to process the Quarterly DepMap-Omics releases from Terra
      data-sciencecancer-genomicscloud-computingdepmap
      HTML
      •23•125•4•3•Updated Feb 5, 2026Feb 5, 2026

    • bibt-gcp-scc

      Public
      Broad Institute BITS Blue Team repository for bibt-gcp-scc PyPI library.
      Python
      •
      MIT License
      •0•0•0•3•Updated Feb 5, 2026Feb 5, 2026

    • faris

      Public
      Server for embeddings of graph nodes
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•5•Updated Feb 5, 2026Feb 5, 2026

    • warp-tools

      Public
      This repository contains all containers that WARP uses.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•12•1•3•Updated Feb 5, 2026Feb 5, 2026

    • adrs

      Public
      Architectural Decision Record tool in Rust
      Rust
      •
      Apache License 2.0
      •6•0•0•1•Updated Feb 5, 2026Feb 5, 2026

    • gnomad_methods

      Public
      Hail helper functions for the gnomAD project and Translational Genomics Group
      genomicsgenomesexomeshail
      Python
      •
      MIT License
      •31•100•9•10•Updated Feb 5, 2026Feb 5, 2026

    • yale

      Public
      Go
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Feb 5, 2026Feb 5, 2026

    • viral-ngs

      Public
      viral-ngs: command line tools and wrappers for processing raw viral genomic data
      pythondockerbioinformaticsgenomicsgenomengsvariant-callingbamgenome-sequencingillumina
      Python
      •
      MIT License
      •67•193•2•0•Updated Feb 5, 2026Feb 5, 2026

    • depmap-omics-wgs

      Public
      Python
      •0•1•3•0•Updated Feb 5, 2026Feb 5, 2026

    • virnucpro-broad

      Public
      This is a custom-version of the VirNucPro tool that has been re-factored to be a more robust/production ready for usage at the Broad.
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 5, 2026Feb 5, 2026

    • pathology-tools

      Public
      Jupyter Notebook
      •0•2•0•3•Updated Feb 5, 2026Feb 5, 2026