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    1.4k repositories

    • poolq

      Public
      The Genetic Perturbation Platform's tool for deconvoluting and quantifying the results of pooled screens
      Scala
      •
      Other
      •1•5•8•2•Updated Feb 4, 2026Feb 4, 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•3•1•Updated Feb 4, 2026Feb 4, 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 4, 2026Feb 4, 2026

    • permutect

      Public
      Permutect, an incredibly efficient deep learning architecture for somatic and germline variant calling
      Python
      •1•8•10•2•Updated Feb 4, 2026Feb 4, 2026

    • seqr-helm

      Public
      Helm charts for the seqr project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•3•4•1•Updated Feb 4, 2026Feb 4, 2026

    • genomeshader

      Public
      Visualization of biobank-scale genomic datasets.
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•4•7•3•Updated Feb 4, 2026Feb 4, 2026

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •23•23•21•4•Updated Feb 4, 2026Feb 4, 2026

    • pyqtl

      Public
      Collection of analysis tools for quantitative trait loci
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •11•61•0•2•Updated Feb 4, 2026Feb 4, 2026

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      TypeScript
      •
      BSD 2-Clause "Simplified" License
      •1•8•1•4•Updated Feb 3, 2026Feb 3, 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 3, 2026Feb 3, 2026

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •93•200•44•5•Updated Feb 3, 2026Feb 3, 2026

    • viral-pipelines

      Public
      viral-ngs: complete pipelines
      WDL
      •
      Other
      •30•72•21•19•Updated Feb 3, 2026Feb 3, 2026

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•1•0•Updated Feb 3, 2026Feb 3, 2026

    • nomadic_wdl

      Public
      WDL
      •0•1•0•0•Updated Feb 3, 2026Feb 3, 2026

    • 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•70•0•3•Updated Feb 3, 2026Feb 3, 2026

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticssparkgenomicsgenomengssequencingdnagatk
      Java
      •
      Other
      •622•1.9k•1.3k•144•Updated Feb 3, 2026Feb 3, 2026

    • backstage

      Public
      Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
      TypeScript
      •0•2•0•0•Updated Feb 3, 2026Feb 3, 2026

    • scp-ingest-pipeline

      Public
      File Ingest Pipeline for Single Cell Portal
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•0•3•Updated Feb 3, 2026Feb 3, 2026

    • gnomad_qc

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •29•69•5•14•Updated Feb 3, 2026Feb 3, 2026

    • poasta

      Public
      Fast and exact gap-affine partial order alignment
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •5•58•9•4•Updated Feb 3, 2026Feb 3, 2026

    • faris

      Public
      Server for embeddings of graph nodes
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•4•Updated Feb 3, 2026Feb 3, 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 3, 2026Feb 3, 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 3, 2026Feb 3, 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 3, 2026Feb 3, 2026

    • gnomad-browser

      Public
      Explore gnomAD datasets on the web
      javascriptgenomicsgnomad
      TypeScript
      •
      MIT License
      •49•86•167•13•Updated Feb 3, 2026Feb 3, 2026

    • ops-terra-utils

      Public
      Python
      •3•6•0•0•Updated Feb 3, 2026Feb 3, 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•13•Updated Feb 3, 2026Feb 3, 2026

    • qprimer_designer

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

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•26•0•5•Updated Feb 3, 2026Feb 3, 2026

    • ml4h

      Public
      Python
      •
      GNU General Public License v3.0
      •29•167•32•24•Updated Feb 3, 2026Feb 3, 2026