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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 615

  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 380

  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 374

Repositories

Showing 10 of 1411 repositories
  • long-read-pipelines Public

    Long read production pipelines

    broadinstitute/long-read-pipelines’s past year of commit activity
    Jupyter Notebook 148 BSD-3-Clause 25 95 (2 issues need help) 26 Updated Oct 7, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 194 AGPL-3.0 90 50 5 Updated Oct 7, 2025
  • celldega Public

    Spatial omics analysis and visualization library

    broadinstitute/celldega’s past year of commit activity
    Jupyter Notebook 18 1 1 44 Updated Oct 6, 2025
  • depmap-omics-wgs Public
    broadinstitute/depmap-omics-wgs’s past year of commit activity
    Python 0 0 3 0 Updated Oct 6, 2025
  • thelma Public
    broadinstitute/thelma’s past year of commit activity
    Go 0 BSD-3-Clause 1 0 10 Updated Oct 6, 2025
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 2 1 0 Updated Oct 6, 2025
  • monorepo Public

    Compendium of tools for the Imaging Platform

    broadinstitute/monorepo’s past year of commit activity
    Python 15 BSD-3-Clause 3 3 2 Updated Oct 6, 2025
  • 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 7 (1 issue needs help) 2 Updated Oct 6, 2025
  • cromwell Public

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

    broadinstitute/cromwell’s past year of commit activity
    Scala 1,039 BSD-3-Clause 374 757 58 Updated Oct 6, 2025
  • backstage Public

    Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)

    broadinstitute/backstage’s past year of commit activity
    TypeScript 2 0 0 3 Updated Oct 6, 2025
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