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@broadinstitute

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 1.8k 604

  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 373

  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 361

Repositories

Showing 10 of 1374 repositories
  • beclust3d-public Public

    BEClust3D public repository

    broadinstitute/beclust3d-public’s past year of commit activity
    Python 0 0 0 0 Updated Apr 14, 2025
  • bibt-containers Public

    Public Docker containers for use with Blue Team tooling.

    broadinstitute/bibt-containers’s past year of commit activity
    Python 0 0 0 0 Updated Apr 14, 2025
  • ops_util_module Public
    broadinstitute/ops_util_module’s past year of commit activity
    Python 0 0 0 0 Updated Apr 14, 2025
  • warp Public

    WDL Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 211 BSD-3-Clause 102 5 14 Updated Apr 14, 2025
  • palantir-workflows Public

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

    broadinstitute/palantir-workflows’s past year of commit activity
    WDL 23 BSD-3-Clause 8 4 3 Updated Apr 14, 2025
  • monorepo Public

    Compendium of tools for the Imaging Platform

    broadinstitute/monorepo’s past year of commit activity
    Python 11 BSD-3-Clause 2 7 0 Updated Apr 14, 2025
  • 2025_varchamp_snakemake Public
    broadinstitute/2025_varchamp_snakemake’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Apr 14, 2025
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 25 BSD-3-Clause 4 0 5 Updated Apr 14, 2025
  • shared-workflows Public

    GitHub Action workflows that can be shared by multiple repositories

    broadinstitute/shared-workflows’s past year of commit activity
    0 BSD-3-Clause 1 3 1 Updated Apr 14, 2025
  • sam Public

    workbench identity and access management

    broadinstitute/sam’s past year of commit activity
    Scala 41 BSD-3-Clause 12 3 31 Updated Apr 14, 2025
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