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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 603

  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 1356 repositories
  • agora Public

    It's a methods repository!

    broadinstitute/agora’s past year of commit activity
    Scala 11 BSD-3-Clause 2 0 1 Updated Mar 28, 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 Mar 28, 2025
  • depmap_omics Public

    What you need to process the Quarterly DepMap-Omics releases from Terra

    broadinstitute/depmap_omics’s past year of commit activity
    HTML 114 22 3 7 Updated Mar 28, 2025
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 26 BSD-3-Clause 4 0 12 Updated Mar 28, 2025
  • dig-aggregator-methods Public

    Monorepo of methods implemented for the Aggregator

    broadinstitute/dig-aggregator-methods’s past year of commit activity
    Python 1 BSD-3-Clause 2 0 7 Updated Mar 28, 2025
  • gnomad_qc Public
    broadinstitute/gnomad_qc’s past year of commit activity
    Jupyter Notebook 69 BSD-3-Clause 27 6 12 Updated Mar 28, 2025
  • seqr-helm Public

    Helm charts for the seqr project

    broadinstitute/seqr-helm’s past year of commit activity
    Python 3 BSD-3-Clause 2 0 0 Updated Mar 28, 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 2 Updated Mar 28, 2025
  • BEClust3D Public
    broadinstitute/BEClust3D’s past year of commit activity
    Jupyter Notebook 0 0 0 8 Updated Mar 28, 2025
  • warp Public

    WDL Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 211 BSD-3-Clause 102 5 12 Updated Mar 27, 2025
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