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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 622

  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 1443 repositories
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 2 1 0 Updated Feb 4, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 225 BSD-3-Clause 112 6 10 Updated Feb 4, 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 5 Updated Feb 4, 2026
  • viral-ngs Public

    viral-ngs: command line tools and wrappers for processing raw viral genomic data

    broadinstitute/viral-ngs’s past year of commit activity
    Python 193 MIT 67 2 0 Updated Feb 4, 2026
  • firecloud-orchestration Public
    broadinstitute/firecloud-orchestration’s past year of commit activity
    Scala 31 BSD-3-Clause 4 0 5 Updated Feb 4, 2026
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 72 30 21 20 Updated Feb 4, 2026
  • gnomad_qc Public
    broadinstitute/gnomad_qc’s past year of commit activity
    Jupyter Notebook 69 BSD-3-Clause 29 5 14 Updated Feb 4, 2026
  • qprimer_designer Public

    Design tool for highly performant qPCR diagnostics.

    broadinstitute/qprimer_designer’s past year of commit activity
    Jupyter Notebook 3 MIT 1 6 2 Updated Feb 4, 2026
  • 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 1,049 BSD-3-Clause 377 757 50 Updated Feb 4, 2026
  • lrma-aou2-panel-creation Public Forked from broadinstitute/lrma-aou1-panel-creation

    Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 2 long-reads callset.

    broadinstitute/lrma-aou2-panel-creation’s past year of commit activity
    Java 0 2 0 2 Updated Feb 4, 2026
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