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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 1.8k 598

  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 995 372

  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 360

Repositories

Showing 10 of 1343 repositories
  • warp Public

    WDL Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 208 BSD-3-Clause 101 7 18 Updated Feb 20, 2025
  • agora Public

    It's a methods repository!

    broadinstitute/agora’s past year of commit activity
    Scala 11 BSD-3-Clause 2 0 2 Updated Feb 20, 2025
  • gnomad-browser Public

    Explore gnomAD datasets on the web

    broadinstitute/gnomad-browser’s past year of commit activity
    TypeScript 81 MIT 46 163 (3 issues need help) 14 Updated Feb 20, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,769 598 1,234 (8 issues need help) 139 Updated Feb 20, 2025
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    Python 7 BSD-2-Clause 1 0 10 Updated Feb 20, 2025
  • BCL-Examples Public

    Storehouse of Scripts to share with our API customers to assist with their interactions with BCL Orders

    broadinstitute/BCL-Examples’s past year of commit activity
    Python 1 0 0 2 Updated Feb 20, 2025
  • lrma-aou1-panel-creation Public

    Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 1 long-reads callset.

    broadinstitute/lrma-aou1-panel-creation’s past year of commit activity
    WDL 1 0 22 2 Updated Feb 20, 2025
  • cromwell Public

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

    broadinstitute/cromwell’s past year of commit activity
    Scala 1,009 BSD-3-Clause 360 744 48 Updated Feb 20, 2025
  • long-read-pipelines Public

    Long read production pipelines

    broadinstitute/long-read-pipelines’s past year of commit activity
    Jupyter Notebook 144 BSD-3-Clause 24 95 (2 issues need help) 26 Updated Feb 20, 2025
  • firecloud-orchestration Public
    broadinstitute/firecloud-orchestration’s past year of commit activity
    Scala 31 BSD-3-Clause 4 0 4 Updated Feb 20, 2025
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