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    1.4k repositories

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticssparkgenomicsgenomengssequencingdnagatk
      Java
      •
      Other
      •619•1.9k•1.3k•144•Updated Nov 24, 2025Nov 24, 2025

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •91•195•51•10•Updated Nov 24, 2025Nov 24, 2025

    • viral-pipelines

      Public
      viral-ngs: complete pipelines
      WDL
      •
      Other
      •29•68•23•17•Updated Nov 24, 2025Nov 24, 2025

    • gnomad_qc

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •28•68•6•11•Updated Nov 24, 2025Nov 24, 2025

    • celldega

      Public
      Spatial omics analysis and visualization library
      Jupyter Notebook
      •
      Other
      •1•21•1•60•Updated Nov 24, 2025Nov 24, 2025

    • warp

      Public
      Warp Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •111•220•6•10•Updated Nov 24, 2025Nov 24, 2025

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•26•0•4•Updated Nov 24, 2025Nov 24, 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 Nov 24, 2025Nov 24, 2025

    • cromwell

      Public
      Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
      dockerapplicationworkflowcloudbioinformaticsscalaexecutorhpccontainerswdl
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •375•1k•757•52•Updated Nov 24, 2025Nov 24, 2025

    • nf-pooled-cellpainting-assets

      Public
      Python
      •2•0•0•0•Updated Nov 24, 2025Nov 24, 2025

    • firecloud-orchestration

      Public
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•31•0•1•Updated Nov 24, 2025Nov 24, 2025

    • nebelung

      Public
      Python wrapper for the Firecloud API
      Python
      •0•3•0•0•Updated Nov 24, 2025Nov 24, 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•2•Updated Nov 24, 2025Nov 24, 2025

    • genetic-prevalence-estimator

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•4•53•1•Updated Nov 24, 2025Nov 24, 2025

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•9•0•19•Updated Nov 24, 2025Nov 24, 2025

    • TRExplorer

      Public
      An online portal for exploring tandem repeats (TRs) genome-wide.
      HTML
      •
      MIT License
      •0•0•5•0•Updated Nov 24, 2025Nov 24, 2025

    • lrma-aou1-panel-creation

      Public
      Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 1 long-reads callset.
      WDL
      •2•1•22•2•Updated Nov 24, 2025Nov 24, 2025

    • monorepo

      Public
      Compendium of tools for the Imaging Platform
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•15•3•2•Updated Nov 24, 2025Nov 24, 2025

    • ddp-study-server

      Public
      Pepper Study Server
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •7•8•1•2•Updated Nov 24, 2025Nov 24, 2025

    • cellpainting-gallery

      Public
      Cell Painting Gallery
      Other
      •16•113•9•1•Updated Nov 24, 2025Nov 24, 2025

    • beehive

      Public
      Beehive is a web UI for interacting with Sherlock, DSP DevOps's deployment source-of-truth service
      reacttypescriptremixtailwindcss
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•0•6•Updated Nov 24, 2025Nov 24, 2025

    • sherlock

      Public
      DSP DevOps's deployment source-of-truth service
      golangpostgresgorm
      Go
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•2•Updated Nov 24, 2025Nov 24, 2025

    • hidive

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•6•1•Updated Nov 23, 2025Nov 23, 2025

    • TissueMosaic_Manuscript

      Public
      Reproduce figures from TissueMosaic Manuscript
      Jupyter Notebook
      •0•0•0•0•Updated Nov 23, 2025Nov 23, 2025

    • str-analysis

      Public
      Scripts and utilities related to analyzing tandem repeats (TRs).
      Python
      •
      MIT License
      •10•41•0•0•Updated Nov 23, 2025Nov 23, 2025

    • palantir-workflows

      Public
      Utility workflows for the DSP hydro.gen team (formerly palantir)
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •10•26•4•2•Updated Nov 23, 2025Nov 23, 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 Nov 22, 2025Nov 22, 2025

    • DropSift

      Public
      cell caller for sn/snRNA sequence data
      R
      •
      Other
      •0•1•0•0•Updated Nov 22, 2025Nov 22, 2025

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •75•196•93•28•Updated Nov 22, 2025Nov 22, 2025

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•1•0•Updated Nov 21, 2025Nov 21, 2025