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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 624

  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 379

Repositories

Showing 10 of 1457 repositories
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 201 BSD-3-Clause 76 97 26 Updated Mar 5, 2026
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 201 AGPL-3.0 93 43 14 Updated Mar 5, 2026
  • ml4h Public
    broadinstitute/ml4h’s past year of commit activity
    Python 168 GPL-3.0 29 32 (1 issue needs help) 26 Updated Mar 5, 2026
  • MDL-workflows Public

    Workflow, utilities and other artefacts developed by or for the Methods Development Lab at the Broad Institute

    broadinstitute/MDL-workflows’s past year of commit activity
    WDL 5 4 1 0 Updated Mar 5, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 225 BSD-3-Clause 112 7 10 Updated Mar 5, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,915 624 1,281 (8 issues need help) 149 Updated Mar 6, 2026
  • orsp-pub Public

    Public ORSP Compliance Portal

    broadinstitute/orsp-pub’s past year of commit activity
    JavaScript 3 BSD-3-Clause 0 0 25 Updated Mar 5, 2026
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 2 0 0 Updated Mar 5, 2026
  • TRExplorer Public

    An online portal for exploring tandem repeats (TRs) genome-wide.

    broadinstitute/TRExplorer’s past year of commit activity
    HTML 1 MIT 0 5 0 Updated Mar 5, 2026
  • dig-local-llm Public
    broadinstitute/dig-local-llm’s past year of commit activity
    Python 0 0 0 0 Updated Mar 5, 2026
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