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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 1436 repositories
  • data-registry-api Public
    broadinstitute/data-registry-api’s past year of commit activity
    Python 1 BSD-3-Clause 1 0 2 Updated Jan 13, 2026
  • SpliceAI-lookup-dev Public

    dev UIs for spliceai-lookup.broadinstitute.org

    broadinstitute/SpliceAI-lookup-dev’s past year of commit activity
    HTML 0 MIT 0 0 0 Updated Jan 13, 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 Jan 13, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,899 622 1,272 (8 issues need help) 142 Updated Jan 13, 2026
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 198 AGPL-3.0 92 45 6 Updated Jan 13, 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 29 Updated Jan 13, 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 1,047 BSD-3-Clause 377 757 50 Updated Jan 13, 2026
  • fiss Public

    FireCloud Service Selector (FISS) -- Python bindings and CLI for FireCloud execution engine

    broadinstitute/fiss’s past year of commit activity
    Python 33 BSD-3-Clause 32 50 3 Updated Jan 13, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 224 BSD-3-Clause 112 6 10 Updated Jan 13, 2026
  • gnomad_qc Public
    broadinstitute/gnomad_qc’s past year of commit activity
    Jupyter Notebook 68 BSD-3-Clause 29 6 12 Updated Jan 13, 2026
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