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    1.4k repositories

    • 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•26•Updated Sep 23, 2025Sep 23, 2025

    • seqr-helm

      Public
      Helm charts for the seqr project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•3•0•Updated Sep 23, 2025Sep 23, 2025

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •22•23•18•2•Updated Sep 23, 2025Sep 23, 2025

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •615•1.9k•1.3k•142•Updated Sep 22, 2025Sep 22, 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 22, 2025Sep 22, 2025

    • gnomad-browser

      Public
      Explore gnomAD datasets on the web
      javascriptgenomicsgnomad
      TypeScript
      •
      MIT License
      •49•84•166•8•Updated Sep 22, 2025Sep 22, 2025

    • backstage

      Public
      Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
      TypeScript
      •0•2•0•3•Updated Sep 22, 2025Sep 22, 2025

    • gnomad-deployments

      Public
      kustomizations for current gnomad project kubernetes deployments
      Makefile
      •1•1•1•4•Updated Sep 22, 2025Sep 22, 2025

    • 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•6•6•Updated Sep 22, 2025Sep 22, 2025

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •90•194•53•5•Updated Sep 22, 2025Sep 22, 2025

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•1•0•Updated Sep 22, 2025Sep 22, 2025

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•25•0•2•Updated Sep 22, 2025Sep 22, 2025

    • BCL-Examples

      Public
      Storehouse of Scripts to share with our API customers to assist with their interactions with BCL Orders
      Python
      •0•1•0•2•Updated Sep 22, 2025Sep 22, 2025

    • mad4hatter_wdls

      Public
      Repo for conversion of mad4hatter pipelines
      WDL
      •0•0•0•2•Updated Sep 22, 2025Sep 22, 2025

    • str-analysis

      Public
      Scripts and utilities related to analyzing short tandem repeats (STRs).
      Python
      •
      MIT License
      •9•39•0•0•Updated Sep 22, 2025Sep 22, 2025

    • warp-tools

      Public
      This repository contains all containers that WARP uses.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•11•1•4•Updated Sep 22, 2025Sep 22, 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 22, 2025Sep 22, 2025

    • shared-workflows

      Public
      GitHub Action workflows that can be shared by multiple repositories
      BSD 3-Clause "New" or "Revised" License
      •1•0•3•1•Updated Sep 22, 2025Sep 22, 2025

    • 2025_varchamp_snakemake

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Sep 22, 2025Sep 22, 2025

    • palantir-workflows

      Public
      Utility workflows for the DSP hydro.gen team (formerly palantir)
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •9•26•4•1•Updated Sep 22, 2025Sep 22, 2025

    • python-sudoers

      Public
      Python library for parsing a Linux sudoers file
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•7•1•1•Updated Sep 22, 2025Sep 22, 2025

    • glama

      Public
      Genomic long-read analysis modules and applications
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•2•Updated Sep 22, 2025Sep 22, 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 22, 2025Sep 22, 2025

    • carpenter-singh-lab-guide

      Public
      BSD 3-Clause "New" or "Revised" License
      •0•1•1•1•Updated Sep 22, 2025Sep 22, 2025

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•9•0•18•Updated Sep 22, 2025Sep 22, 2025

    • TAG-public

      Public
      Official workflows published by the Broad Institute's Genomics Platform Translation Analysis Group (TAG)
      WDL
      •3•5•1•18•Updated Sep 22, 2025Sep 22, 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 22, 2025Sep 22, 2025

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•8•0•8•Updated Sep 22, 2025Sep 22, 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 Sep 22, 2025Sep 22, 2025

    • Drop-seq

      Public
      Java tools for analyzing Drop-seq data
      Jupyter Notebook
      •
      MIT License
      •35•130•17•1•Updated Sep 22, 2025Sep 22, 2025