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    1.4k repositories

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •75•196•92•29•Updated Dec 9, 2025Dec 9, 2025

    • str-analysis

      Public
      Scripts and utilities related to analyzing tandem repeats (TRs).
      Python
      •
      MIT License
      •10•41•0•0•Updated Dec 9, 2025Dec 9, 2025

    • warp

      Public
      Warp Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •112•221•6•11•Updated Dec 9, 2025Dec 9, 2025

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticssparkgenomicsgenomengssequencingdnagatk
      Java
      •
      Other
      •621•1.9k•1.3k•145•Updated Dec 9, 2025Dec 9, 2025

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      TypeScript
      •
      BSD 2-Clause "Simplified" License
      •1•8•1•12•Updated Dec 9, 2025Dec 9, 2025

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •92•197•51•10•Updated Dec 9, 2025Dec 9, 2025

    • warp-tools

      Public
      This repository contains all containers that WARP uses.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•12•1•3•Updated Dec 9, 2025Dec 9, 2025

    • cellpainting-gallery

      Public
      Cell Painting Gallery
      Other
      •16•115•9•2•Updated Dec 9, 2025Dec 9, 2025

    • haplograph

      Public
      WDL
      •
      MIT License
      •0•0•0•0•Updated Dec 8, 2025Dec 8, 2025

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •22•23•20•5•Updated Dec 8, 2025Dec 8, 2025

    • gnomad_qc

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •28•68•6•15•Updated Dec 8, 2025Dec 8, 2025

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•26•0•5•Updated Dec 8, 2025Dec 8, 2025

    • gnomad_methods

      Public
      Hail helper functions for the gnomAD project and Translational Genomics Group
      genomicsgenomesexomeshail
      Python
      •
      MIT License
      •31•97•9•11•Updated Dec 8, 2025Dec 8, 2025

    • backstage

      Public
      Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
      TypeScript
      •0•2•2•1•Updated Dec 8, 2025Dec 8, 2025

    • protigy-v2

      Public
      ProTIGY - Proteogenomics Toolset for Integrative Data Analysis
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•11•0•Updated Dec 8, 2025Dec 8, 2025

    • sam

      Public
      workbench identity and access management
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •12•42•3•7•Updated Dec 8, 2025Dec 8, 2025

    • 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•68•0•0•Updated Dec 8, 2025Dec 8, 2025

    • taiga

      Public
      Taiga for Dataset management
      Python
      •1•12•0•0•Updated Dec 8, 2025Dec 8, 2025

    • long-read-pipelines

      Public
      Long read production pipelines
      pipelineswdlvariant-callingde-novo-assemblylong-reads
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •25•150•95•25•Updated Dec 8, 2025Dec 8, 2025

    • orsp-pub

      Public
      Public ORSP Compliance Portal
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•25•Updated Dec 8, 2025Dec 8, 2025

    • TRExplorer

      Public
      An online portal for exploring tandem repeats (TRs) genome-wide.
      HTML
      •
      MIT License
      •0•0•3•0•Updated Dec 8, 2025Dec 8, 2025

    • scp-ingest-pipeline

      Public
      File Ingest Pipeline for Single Cell Portal
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•0•1•Updated Dec 8, 2025Dec 8, 2025

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•1•1•Updated Dec 8, 2025Dec 8, 2025

    • genetics-kp-dev

      Public
      Python
      •
      MIT License
      •3•0•28•7•Updated Dec 8, 2025Dec 8, 2025

    • glama

      Public
      Genomic long-read analysis modules and applications
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•2•Updated Dec 8, 2025Dec 8, 2025

    • jump-profiling-recipe

      Public
      Workflow for processing cpg0016-jump profiles
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•4•9•1•Updated Dec 8, 2025Dec 8, 2025

    • carpenter-singh-lab-guide

      Public
      BSD 3-Clause "New" or "Revised" License
      •0•1•2•1•Updated Dec 8, 2025Dec 8, 2025

    • poolq

      Public
      The Genetic Perturbation Platform's tool for deconvoluting and quantifying the results of pooled screens
      Scala
      •
      Other
      •1•5•8•1•Updated Dec 8, 2025Dec 8, 2025

    • ops-terra-utils

      Public
      Python
      •3•6•0•1•Updated Dec 8, 2025Dec 8, 2025

    • bican-mccarroll-manuscript1

      Public
      Scripts used to process data for the first McCarroll lab BICAN manuscript
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 8, 2025Dec 8, 2025