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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 622

  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 381

  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 377

Repositories

Showing 10 of 1436 repositories
  • 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 1 16 Updated Jan 13, 2026
  • puppet-sentinelone_agent Public

    Puppet module to manage the SentinelOne agent

    broadinstitute/puppet-sentinelone_agent’s past year of commit activity
    Ruby 2 BSD-3-Clause 4 1 1 Updated Jan 13, 2026
  • trexplorer-catalog Public

    Genome-wide TR catalog and variation clusters described in [Weisburd, Dolzhenko, et al. 2024]

    broadinstitute/trexplorer-catalog’s past year of commit activity
    Python 17 MIT 1 0 0 Updated Jan 13, 2026
  • backstage Public

    Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)

    broadinstitute/backstage’s past year of commit activity
    TypeScript 2 0 1 4 Updated Jan 13, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 224 BSD-3-Clause 112 6 10 Updated Jan 13, 2026
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 70 30 21 18 Updated Jan 13, 2026
  • viral-classify Public

    viral-ngs: taxonomic identification, classification, and filtering steps

    broadinstitute/viral-classify’s past year of commit activity
    Python 3 0 3 2 Updated Jan 13, 2026
  • viral-phylo Public

    viral-ngs: phylogenetics, annotation, intrahost variants

    broadinstitute/viral-phylo’s past year of commit activity
    Python 4 0 8 2 Updated Jan 13, 2026
  • genomeshader Public

    Visualization of biobank-scale genomic datasets.

    broadinstitute/genomeshader’s past year of commit activity
    HTML 4 BSD-3-Clause 0 7 (2 issues need help) 3 Updated Jan 13, 2026
  • 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 2 Updated Jan 13, 2026
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