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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 2k 631

  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 1.1k 386

  3. cromwell cromwell Public

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

    Scala 1.1k 382

Repositories

Showing 10 of 1548 repositories
  • single_cell_portal_core Public

    Rails/Docker application for the Broad Institute's single cell RNA-seq data portal

    broadinstitute/single_cell_portal_core's past year of commit activity
    Ruby 76 BSD-3-Clause 30 0 3 Updated Oct 27, 2026
  • scp-ingest-pipeline Public

    File Ingest Pipeline for Single Cell Portal

    broadinstitute/scp-ingest-pipeline's past year of commit activity
    Jupyter Notebook 6 BSD-3-Clause 0 0 2 Updated Oct 27, 2026
  • via Public

    A new variant interpretation tool for the All of Us Researcher Workbench, leveraging linked genomic and phenotypic data to support clinical classification

    broadinstitute/via's past year of commit activity
    TypeScript 2 0 0 5 Updated Oct 27, 2026
  • 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 2 1 8 Updated Oct 27, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp's past year of commit activity
    Jupyter Notebook 232 BSD-3-Clause 118 13 29 Updated Oct 27, 2026
  • celldega Public

    Spatial and multiomic visualization and analysis library

    broadinstitute/celldega's past year of commit activity
    Jupyter Notebook 79 7 1 62 Updated Oct 27, 2026
  • PrimerCast Public

    Design tool for highly performant qPCR diagnostics.

    broadinstitute/PrimerCast's past year of commit activity
    Python 12 MIT 1 4 0 Updated Oct 27, 2026
  • gnomad_qc Public
    broadinstitute/gnomad_qc's past year of commit activity
    Jupyter Notebook 71 BSD-3-Clause 32 5 12 Updated Oct 27, 2026
  • gnomad-deployments Public

    kustomizations for current gnomad project kubernetes deployments

    broadinstitute/gnomad-deployments's past year of commit activity
    Makefile 1 1 0 2 Updated Oct 28, 2026
  • gnomad-browser-toolkit Public

    Components for building genomic data browsers

    broadinstitute/gnomad-browser-toolkit's past year of commit activity
    JavaScript 10 MIT 5 7 3 Updated Oct 27, 2026
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