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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 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
  • celldega Public

    Spatial omics analysis and visualization library

    broadinstitute/celldega’s past year of commit activity
    Jupyter Notebook 5 0 1 14 Updated Apr 15, 2025
  • juniper Public
    broadinstitute/juniper’s past year of commit activity
    Java 9 BSD-3-Clause 5 0 15 Updated Apr 15, 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 1,012 BSD-3-Clause 361 746 49 Updated Apr 15, 2025
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    Python 8 BSD-2-Clause 1 0 9 Updated Apr 15, 2025
  • seqr-loading-pipelines Public

    hail-based pipelines for annotating variant callsets and exporting them to elasticsearch

    broadinstitute/seqr-loading-pipelines’s past year of commit activity
    Python 23 MIT 20 23 4 Updated Apr 15, 2025
  • firecloud-orchestration Public
    broadinstitute/firecloud-orchestration’s past year of commit activity
    Scala 31 BSD-3-Clause 4 0 1 Updated Apr 15, 2025
  • warp Public

    WDL Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 211 BSD-3-Clause 102 5 13 Updated Apr 15, 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 0 Updated Apr 15, 2025
  • python-sudoers Public

    Python library for parsing a Linux sudoers file

    broadinstitute/python-sudoers’s past year of commit activity
    Python 7 BSD-3-Clause 7 2 0 Updated Apr 15, 2025
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 1 1 0 Updated Apr 15, 2025
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