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    1.5k repositories

    • 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 19, 2026Apr 19, 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 19, 2026Apr 19, 2026

    • Drop-seq-wdl

      Public
      WDL
      •
      MIT License
      •0•0•1•0•Updated Apr 19, 2026Apr 19, 2026

    • Himito

      Public
      WDL
      •
      MIT License
      •2•9•0•0•Updated Apr 19, 2026Apr 19, 2026

    • BE3D

      Public
      BE3D public repository
      Python
      •
      MIT License
      •0•1•2•0•Updated Apr 18, 2026Apr 18, 2026

    • qprimer_designer

      Public
      Design tool for highly performant qPCR diagnostics.
      Python
      •
      MIT License
      •1•6•5•0•Updated Apr 18, 2026Apr 18, 2026

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsspark
      sciencebioinformaticssparkgenomicsgenomengssequencingdnagatk
      Java
      •
      Other
      •624•1.9k•1.3k•145•Updated Apr 18, 2026Apr 18, 2026

    • ml4h

      Public
      Python
      •
      GNU General Public License v3.0
      •24•169•33•25•Updated Apr 18, 2026Apr 18, 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 Apr 18, 2026Apr 18, 2026

    • orsp-pub

      Public
      Public ORSP Compliance Portal
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•25•Updated Apr 18, 2026Apr 18, 2026

    • GeneTEA

      Public
      Gene-Term Enrichment Analysis (GeneTEA)
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •2•10•0•6•Updated Apr 18, 2026Apr 18, 2026

    • sendgrid-java

      Public
      Broad Institute fork of the Official Twilio SendGrid Led, Community Driven Java API Library
      Java
      •
      MIT License
      •407•0•0•2•Updated Apr 18, 2026Apr 18, 2026

    • warp

      Public
      Warp Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •115•225•7•20•Updated Apr 18, 2026Apr 18, 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•3•0•0•Updated Apr 17, 2026Apr 17, 2026

    • cromwell

      Public
      Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
      dockerapplicationworkflow
      dockerapplicationworkflowcloudbioinformaticsscalaexecutorhpccontainerswdl
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •381•1.1k•762•49•Updated Apr 17, 2026Apr 17, 2026

    • cellpainting-gallery-metadata

      Public
      Project to create metadata that is harmonized across the Cell Painting Gallery
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•4•0•Updated Apr 17, 2026Apr 17, 2026

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•0•1•Updated Apr 17, 2026Apr 17, 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)
      WDL
      •
      MIT License
      •0•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • broad-nnfc-hiPSC-to-EC

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • DepMap-NextGen-Public

      Public
      Python
      •0•1•0•0•Updated Apr 17, 2026Apr 17, 2026

    • carmen-analysis

      Public
      Python
      •
      MIT License
      •0•4•2•0•Updated Apr 17, 2026Apr 17, 2026

    • warp-tools

      Public
      This repository contains all containers that WARP uses.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•13•1•6•Updated Apr 17, 2026Apr 17, 2026

    • ga4gh-fedml-hackathon-connect2026

      Public
      Fed ML Hackathon in Connect 2026
      Apache License 2.0
      •9•0•0•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•30•8•0•Updated Apr 17, 2026Apr 17, 2026

    • bitstore-app

      Public
      BITStore AppEngine App
      Python
      •1•1•4•6•Updated Apr 17, 2026Apr 17, 2026

    • backstage

      Public
      Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
      TypeScript
      •0•2•0•0•Updated Apr 17, 2026Apr 17, 2026

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •94•204•46•10•Updated Apr 17, 2026Apr 17, 2026

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      TypeScript
      •
      BSD 2-Clause "Simplified" License
      •2•8•1•2•Updated Apr 17, 2026Apr 17, 2026

    • gnomad_qc

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •31•70•5•14•Updated Apr 17, 2026Apr 17, 2026

    • celldega

      Public
      Spatial omics analysis and visualization library
      Jupyter Notebook
      •
      Other
      •2•25•2•55•Updated Apr 17, 2026Apr 17, 2026
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