Skip to content

@broadinstitute Broad Institute

Change the repository type filter

All

    Repositories list

    1.4k repositories

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •77•193•87•35•Updated Sep 2, 2025Sep 2, 2025

    • long-read-pipelines

      Public
      Long read production pipelines
      pipelineswdlvariant-callingde-novo-assemblylong-reads
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •25•147•95•26•Updated Sep 2, 2025Sep 2, 2025

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •22•23•24•4•Updated Sep 2, 2025Sep 2, 2025

    • shared-workflows

      Public
      GitHub Action workflows that can be shared by multiple repositories
      BSD 3-Clause "New" or "Revised" License
      •1•0•3•0•Updated Sep 2, 2025Sep 2, 2025

    • hidive

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•6•1•Updated Sep 1, 2025Sep 1, 2025

    • MicroSplit-reproducibility

      Public
      Notebooks, scripts and utilities to reproduce MicroSplit
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•0•0•0•Updated Sep 1, 2025Sep 1, 2025

    • glama

      Public
      Genomic long-read analysis modules and applications
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•2•Updated Sep 1, 2025Sep 1, 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 1, 2025Sep 1, 2025

    • carpenter-singh-lab-guide

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

    • data-registry

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•10•Updated Sep 1, 2025Sep 1, 2025

    • data-registry-api

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

    • seqr-helm

      Public
      Helm charts for the seqr project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•2•0•Updated Sep 1, 2025Sep 1, 2025

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•25•0•4•Updated Sep 1, 2025Sep 1, 2025

    • sam

      Public
      workbench identity and access management
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •12•41•3•10•Updated Sep 1, 2025Sep 1, 2025

    • firecloud-orchestration

      Public
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•31•0•5•Updated Sep 1, 2025Sep 1, 2025

    • str-analysis

      Public
      Scripts and utilities related to analyzing short tandem repeats (STRs).
      Python
      •
      MIT License
      •9•39•0•0•Updated Sep 1, 2025Sep 1, 2025

    • python-cert_manager

      Public
      Python interface to the Sectigo Certificate Manager REST API
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •23•39•2•2•Updated Sep 1, 2025Sep 1, 2025

    • bits-appengine

      Public
      BITS AppEngine Python Package
      Python
      •0•0•0•1•Updated Sep 1, 2025Sep 1, 2025

    • sherlock

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

    • poolq

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

    • 2025_varchamp_snakemake

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Sep 1, 2025Sep 1, 2025

    • starrynight

      Public
      A toolkit for processing, analyzing, and managing optical pooled screening (OPS) image data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•8•0•2•Updated Aug 31, 2025Aug 31, 2025

    • dig-portal-ai

      Public
      Framework for applying LLMs to A2F Knowledge Portals
      Python
      •
      Apache License 2.0
      •1•0•0•9•Updated Aug 30, 2025Aug 30, 2025

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•8•0•13•Updated Aug 29, 2025Aug 29, 2025

    • backstage

      Public
      Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
      TypeScript
      •0•2•0•0•Updated Aug 29, 2025Aug 29, 2025

    • PANOPLY

      Public
      Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)
      R
      •
      Other
      •16•37•0•1•Updated Aug 29, 2025Aug 29, 2025

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •611•1.8k•1.3k•140•Updated Aug 29, 2025Aug 29, 2025

    • faris

      Public
      Server for embeddings of graph nodes
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•2•Updated Aug 29, 2025Aug 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
      •373•1k•755•54•Updated Aug 29, 2025Aug 29, 2025

    • warp

      Public
      Warp Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •110•215•5•10•Updated Aug 29, 2025Aug 29, 2025