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Broad Institute

Broad Institute of MIT and Harvard

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  1. gatk gatk Public

    Official code repository for GATK versions 4 and up

    Java 1.9k 623

  2. picard picard Public

    A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

    Java 1k 381

  3. cromwell cromwell Public

    Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

    Scala 1k 377

Repositories

Showing 10 of 1439 repositories
  • monorepo Public

    Compendium of tools for the Imaging Platform

    broadinstitute/monorepo’s past year of commit activity
    Python 15 BSD-3-Clause 5 0 1 Updated Jan 17, 2026
  • Dig-GearsGNN Public Forked from snap-stanford/GEARS

    GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations

    broadinstitute/Dig-GearsGNN’s past year of commit activity
    Python 0 MIT 80 0 0 Updated Jan 17, 2026
  • viral-references Public

    Reference tables for viral genomics

    broadinstitute/viral-references’s past year of commit activity
    5 BSD-2-Clause 2 0 1 Updated Jan 17, 2026
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 200 BSD-3-Clause 76 94 30 Updated Jan 17, 2026
  • poolq Public

    The Genetic Perturbation Platform's tool for deconvoluting and quantifying the results of pooled screens

    broadinstitute/poolq’s past year of commit activity
    Scala 5 1 8 (1 issue needs help) 2 Updated Jan 17, 2026
  • qprimer_designer Public

    Design tool for highly performant qPCR diagnostics.

    broadinstitute/qprimer_designer’s past year of commit activity
    Jupyter Notebook 1 MIT 0 8 0 Updated Jan 17, 2026
  • starrynight Public

    A toolkit for processing, analyzing, and managing optical pooled screening (OPS) image data.

    broadinstitute/starrynight’s past year of commit activity
    Python 9 BSD-3-Clause 5 0 7 Updated Jan 17, 2026
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    TypeScript 8 BSD-2-Clause 1 1 8 Updated Jan 17, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,898 623 1,273 (8 issues need help) 143 Updated Jan 17, 2026
  • dsp-appsec-infrastructure-apps Public

    This repository hosts DSP AppSec internal infrastructure apps deployed in GKE.

    broadinstitute/dsp-appsec-infrastructure-apps’s past year of commit activity
    Python 7 BSD-3-Clause 2 0 12 Updated Jan 16, 2026
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