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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 2k 626

  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 1.1k 385

  3. cromwell cromwell Public

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

    Scala 1.1k 381

Repositories

Showing 10 of 1536 repositories
  • ml4h Public
    broadinstitute/ml4h's past year of commit activity
    Python 179 GPL-3.0 11 33 (1 issue needs help) 28 Updated Sep 14, 2026
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr's past year of commit activity
    Python 218 AGPL-3.0 97 45 7 Updated Sep 14, 2026
  • gnomad_qc Public
    broadinstitute/gnomad_qc's past year of commit activity
    Jupyter Notebook 70 BSD-3-Clause 31 5 16 Updated Sep 14, 2026
  • via Public

    A new variant interpretation tool for the All of Us Researcher Workbench, leveraging linked genomic and phenotypic data to support clinical classification

    broadinstitute/via's past year of commit activity
    TypeScript 2 0 0 3 Updated Sep 14, 2026
  • gnomad_methods Public

    Hail helper functions for the gnomAD project and Translational Genomics Group

    broadinstitute/gnomad_methods's past year of commit activity
    Python 102 MIT 32 8 10 Updated Sep 14, 2026
  • cheesemonger Public

    A storage system for large perturb seq data

    broadinstitute/cheesemonger's past year of commit activity
    Python 0 0 0 2 Updated Sep 14, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp's past year of commit activity
    Jupyter Notebook 230 BSD-3-Clause 118 13 20 Updated Sep 14, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk's past year of commit activity
    Java 1,998 626 1,292 (8 issues need help) 154 Updated Sep 14, 2026
  • jump-profiling-recipe Public

    Workflow for processing cpg0016-jump profiles

    broadinstitute/jump-profiling-recipe's past year of commit activity
    Python 5 BSD-3-Clause 8 9 1 Updated Sep 14, 2026
  • glama Public

    Genomic long-read analysis modules and applications

    broadinstitute/glama's past year of commit activity
    Rust 0 BSD-3-Clause 0 0 2 Updated Sep 14, 2026
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