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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 617

  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 1416 repositories
  • thurloe Public

    A simple service to store arbitrary key/value pairs

    broadinstitute/thurloe’s past year of commit activity
    Scala 3 BSD-3-Clause 0 0 1 Updated Nov 1, 2025
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 25 BSD-3-Clause 4 0 4 Updated Nov 1, 2025
  • sam Public

    workbench identity and access management

    broadinstitute/sam’s past year of commit activity
    Scala 41 BSD-3-Clause 12 3 10 Updated Nov 1, 2025
  • firecloud-orchestration Public
    broadinstitute/firecloud-orchestration’s past year of commit activity
    Scala 31 BSD-3-Clause 4 0 2 Updated Nov 1, 2025
  • TRExplorer Public

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

    broadinstitute/TRExplorer’s past year of commit activity
    HTML 0 MIT 0 6 0 Updated Oct 31, 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 31, 2025
  • 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 0 8 Updated Oct 31, 2025
  • bmxp Public

    The tools that constitute a nontargeted LCMS metabolomics data processing pipeline, created and used by the Broad Institute Metabolomics Platform.

    broadinstitute/bmxp’s past year of commit activity
    Python 13 0 0 0 Updated Oct 31, 2025
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 195 AGPL-3.0 89 52 5 Updated Oct 31, 2025
  • depmap-omics-long-read-rna Public
    broadinstitute/depmap-omics-long-read-rna’s past year of commit activity
    Python 2 0 0 0 Updated Oct 31, 2025
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