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    • BE3D

      Public
      BE3D public repository
      Python
      •
      MIT License
      •0•1•2•0•Updated Apr 17, 2026Apr 17, 2026

    • SpliceAI-lookup

      Public
      Website for checking the SpliceAI, Pangolin, and other predictor scores for variant(s) of interest.
      pangolinspliceai
      pangolinspliceai
      HTML
      •
      MIT License
      •10•29•8•0•Updated Apr 17, 2026Apr 17, 2026

    • SpliceAI-lookup-dev

      Public
      dev. version of the spliceai-lookup.broadinstitute.org website
      HTML
      •
      MIT License
      •0•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variation
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •76•202•98•30•Updated Apr 16, 2026Apr 16, 2026

    • sherlock

      Public
      DSP DevOps's deployment source-of-truth service
      golangpostgresgorm
      golangpostgresgorm
      Go
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•24•Updated Apr 16, 2026Apr 16, 2026

    • popout

      Public
      GPU-accelerated local ancestry inference at biobank scale, no reference panel required.
      Python
      •0•2•0•0•Updated Apr 16, 2026Apr 16, 2026

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •94•204•46•11•Updated Apr 16, 2026Apr 16, 2026

    • long-read-pipelines

      Public
      Long read production pipelines
      pipelineswdlvariant-calling
      pipelineswdlvariant-callingde-novo-assemblylong-reads
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •25•151•95•25•Updated Apr 16, 2026Apr 16, 2026

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      TypeScript
      •
      BSD 2-Clause "Simplified" License
      •2•8•1•2•Updated Apr 16, 2026Apr 16, 2026

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•0•0•Updated Apr 16, 2026Apr 16, 2026

    • qprimer_designer

      Public
      Design tool for highly performant qPCR diagnostics.
      Python
      •
      MIT License
      •1•6•5•0•Updated Apr 16, 2026Apr 16, 2026

    • warp

      Public
      Warp Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •115•225•7•21•Updated Apr 16, 2026Apr 16, 2026

    • regional_missense_constraint

      Public
      Code to calculate regional missense constraint
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•13•0•0•Updated Apr 16, 2026Apr 16, 2026

    • gnomad_qc

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •31•70•5•15•Updated Apr 16, 2026Apr 16, 2026

    • monorepo

      Public
      Compendium of tools for the Imaging Platform
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•15•1•2•Updated Apr 16, 2026Apr 16, 2026

    • broad-nnfc-hiPSC-to-EC

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • jx

      Public
      JUMP eXplore — skill library and marimo notebook catalog for working with JUMP Cell Painting data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Apr 16, 2026Apr 16, 2026

    • seqr-helm

      Public
      Helm charts for the seqr project
      Go Template
      •
      BSD 3-Clause "New" or "Revised" License
      •6•3•5•2•Updated Apr 16, 2026Apr 16, 2026

    • Himito

      Public
      WDL
      •
      MIT License
      •2•9•0•1•Updated Apr 16, 2026Apr 16, 2026

    • permutect

      Public
      Permutect, an incredibly efficient deep learning architecture for somatic and germline variant calling
      Python
      •
      Apache License 2.0
      •2•12•10•1•Updated Apr 16, 2026Apr 16, 2026

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•9•0•22•Updated Apr 16, 2026Apr 16, 2026

    • bmxp

      Public
      The tools that constitute a nontargeted LCMS metabolomics data processing pipeline, created and used by the Broad Institute Metabolomics Platform.
      C
      •
      Other
      •0•13•0•0•Updated Apr 16, 2026Apr 16, 2026

    • somatic-exome-validation-2026

      Public
      Code used for figures in clinical somatic exome validation (Tsuji & Rickles-Young et al. in npj Genomic Medicine 2026)
      MIT License
      •0•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsspark
      sciencebioinformaticssparkgenomicsgenomengssequencingdnagatk
      Java
      •
      Other
      •624•1.9k•1.3k•144•Updated Apr 16, 2026Apr 16, 2026

    • orsp-pub

      Public
      Public ORSP Compliance Portal
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•25•Updated Apr 16, 2026Apr 16, 2026

    • palantir-workflows

      Public
      Utility workflows for the DSP hydro.gen team (formerly palantir)
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •12•27•4•2•Updated Apr 16, 2026Apr 16, 2026

    • depmap-omics-pipelines-public

      Public
      Workflows for DepMap Omics
      WDL
      •0•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • lrma-aou2-panel-creation

      Public
      Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 2 long-reads callset.
      Java
      •2•0•0•2•Updated Apr 16, 2026Apr 16, 2026

    • dsp-appsec-infrastructure-apps

      Public
      This repository hosts DSP AppSec internal infrastructure apps deployed in GKE.
      securityapplication-securityappsec
      securityapplication-securityappsecsecurity-scannersecure-developmentsecurity-automationsecurity-toolsdevsecopssecurity-scanappsecurity
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•7•0•20•Updated Apr 16, 2026Apr 16, 2026

    • protigy-v2

      Public
      ProTIGY - Proteogenomics Toolset for Integrative Data Analysis
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•7•5•Updated Apr 16, 2026Apr 16, 2026
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