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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 625

  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 382

  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 1464 repositories
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,929 625 1,283 (8 issues need help) 145 Updated Apr 5, 2026
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 202 BSD-3-Clause 75 98 30 Updated Apr 5, 2026
  • beehive Public

    Beehive is a web UI for interacting with Sherlock, DSP DevOps's deployment source-of-truth service

    broadinstitute/beehive’s past year of commit activity
    TypeScript 3 BSD-3-Clause 1 0 19 Updated Apr 5, 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 100 MIT 32 9 9 Updated Apr 4, 2026
  • palantir-workflows Public

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

    broadinstitute/palantir-workflows’s past year of commit activity
    WDL 27 BSD-3-Clause 12 4 2 Updated Apr 4, 2026
  • CODECsuite Public

    analysis pipeline for CODEC data

    broadinstitute/CODECsuite’s past year of commit activity
    C++ 13 7 4 1 Updated Apr 4, 2026
  • popout Public

    GPU-accelerated local ancestry inference at biobank scale, no reference panel required.

    broadinstitute/popout’s past year of commit activity
    Python 2 0 0 0 Updated Apr 4, 2026
  • 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 2 Updated Apr 4, 2026
  • delphy-2026-paper-data Public

    Benchmark data and run results for 2026 Delphy paper

    broadinstitute/delphy-2026-paper-data’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Apr 4, 2026
  • Drop-seq-wdl Public
    broadinstitute/Drop-seq-wdl’s past year of commit activity
    WDL 0 MIT 0 1 0 Updated Apr 4, 2026
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