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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 616

  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 1412 repositories
  • gnomad-browser Public

    Explore gnomAD datasets on the web

    broadinstitute/gnomad-browser’s past year of commit activity
    TypeScript 85 MIT 49 167 (3 issues need help) 8 Updated Oct 17, 2025
  • gnomad-deployments Public

    kustomizations for current gnomad project kubernetes deployments

    broadinstitute/gnomad-deployments’s past year of commit activity
    Makefile 1 1 0 3 Updated Oct 17, 2025
  • ml4h Public
    broadinstitute/ml4h’s past year of commit activity
    Python 148 27 30 (1 issue needs help) 25 Updated Oct 17, 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 55 Updated Oct 17, 2025
  • gnomad_qc Public
    broadinstitute/gnomad_qc’s past year of commit activity
    Jupyter Notebook 68 BSD-3-Clause 28 6 10 Updated Oct 17, 2025
  • nf-pooled-cellpainting-infra Public
    broadinstitute/nf-pooled-cellpainting-infra’s past year of commit activity
    Python 0 0 0 0 Updated Oct 17, 2025
  • palantir-workflows Public

    Utility workflows for the DSP hydro.gen team (formerly palantir)

    broadinstitute/palantir-workflows’s past year of commit activity
    WDL 26 BSD-3-Clause 9 4 0 Updated Oct 17, 2025
  • mad4hatter_wdls Public

    Repo for conversion of mad4hatter pipelines

    broadinstitute/mad4hatter_wdls’s past year of commit activity
    WDL 0 0 0 1 Updated Oct 17, 2025
  • long-read-pipelines Public

    Long read production pipelines

    broadinstitute/long-read-pipelines’s past year of commit activity
    Jupyter Notebook 149 BSD-3-Clause 25 95 (2 issues need help) 25 Updated Oct 17, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,859 616 1,268 (8 issues need help) 142 Updated Oct 17, 2025
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