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    1.5k repositories

    • 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•1•Updated Apr 8, 2026Apr 8, 2026

    • popout

      Public
      GPU-accelerated local ancestry inference at biobank scale, no reference panel required.
      Python
      •0•2•0•0•Updated Apr 8, 2026Apr 8, 2026

    • Himito

      Public
      WDL
      •
      MIT License
      •2•9•0•0•Updated Apr 8, 2026Apr 8, 2026

    • warp

      Public
      Warp Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •115•225•7•16•Updated Apr 8, 2026Apr 8, 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
      •75•202•99•30•Updated Apr 8, 2026Apr 8, 2026

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsspark
      sciencebioinformaticssparkgenomicsgenomengssequencingdnagatk
      Java
      •
      Other
      •625•1.9k•1.3k•145•Updated Apr 8, 2026Apr 8, 2026

    • viral-pipelines

      Public
      viral-ngs: complete pipelines
      WDL
      •
      Other
      •30•73•20•16•Updated Apr 8, 2026Apr 8, 2026

    • bican-mccarroll-manuscript1

      Public
      Scripts used to process data for the first McCarroll lab BICAN manuscript
      R
      •
      MIT License
      •0•0•0•4•Updated Apr 7, 2026Apr 7, 2026

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      TypeScript
      •
      BSD 2-Clause "Simplified" License
      •2•8•1•5•Updated Apr 7, 2026Apr 7, 2026

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •94•203•43•11•Updated Apr 7, 2026Apr 7, 2026

    • dig-bioindex

      Public
      BIO index for genetic records stored in S3 and FastAPI server.
      ot2od036440
      ot2od036440
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•6•0•7•Updated Apr 7, 2026Apr 7, 2026

    • chronos

      Public
      Modeling of time series data for CRISPR KO experiments
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •12•38•0•0•Updated Apr 7, 2026Apr 7, 2026

    • CytominerSqliteMaxColUp2

      Public
      CytominingSqliteMaxColUp2
      WDL
      •0•0•0•0•Updated Apr 7, 2026Apr 7, 2026

    • backstage

      Public
      Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
      TypeScript
      •0•2•0•3•Updated Apr 7, 2026Apr 7, 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 7, 2026Apr 7, 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
      rna-seq-analysissingle-cell-genomicshuman-cell-atlas
      Ruby
      •
      BSD 3-Clause "New" or "Revised" License
      •27•70•0•2•Updated Apr 7, 2026Apr 7, 2026

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •25•23•20•5•Updated Apr 7, 2026Apr 7, 2026

    • gnomad-blog

      Public
      Blog for the gnomAD project
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•4•7•2•Updated Apr 7, 2026Apr 7, 2026

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•0•0•Updated Apr 7, 2026Apr 7, 2026

    • ops-terra-utils

      Public
      Python
      •3•6•0•1•Updated Apr 7, 2026Apr 7, 2026

    • exome-results-browsers

      Public
      Results browsers for case-control studies of psychiatric diseases done at the Broad Institute
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •4•11•8•5•Updated Apr 7, 2026Apr 7, 2026

    • ml4h

      Public
      Python
      •
      GNU General Public License v3.0
      •24•169•33•24•Updated Apr 7, 2026Apr 7, 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 7, 2026Apr 7, 2026

    • taiga

      Public
      Taiga for Dataset management
      Python
      •1•12•0•0•Updated Apr 7, 2026Apr 7, 2026

    • protigy-v2

      Public
      ProTIGY - Proteogenomics Toolset for Integrative Data Analysis
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•6•2•Updated Apr 7, 2026Apr 7, 2026

    • gnomad-browser

      Public
      Explore gnomAD datasets on the web
      javascriptgenomicsgnomad
      javascriptgenomicsgnomad
      TypeScript
      •
      MIT License
      •49•87•168•17•Updated Apr 7, 2026Apr 7, 2026

    • PANOPLY

      Public
      Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)
      WDL
      •
      Other
      •16•38•0•2•Updated Apr 7, 2026Apr 7, 2026

    • missense-pfes

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Apr 7, 2026Apr 7, 2026

    • gnomad_methods

      Public
      Hail helper functions for the gnomAD project and Translational Genomics Group
      genomicsgenomesexomes
      genomicsgenomesexomeshail
      Python
      •
      MIT License
      •32•100•9•10•Updated Apr 7, 2026Apr 7, 2026

    • Drop-seq

      Public
      Java tools for analyzing Drop-seq data
      Jupyter Notebook
      •
      MIT License
      •35•135•11•0•Updated Apr 7, 2026Apr 7, 2026
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