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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 1.9k 623

  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 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 1.1k 378

Repositories

Showing 10 of 1449 repositories
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp’s past year of commit activity
    WDL 225 BSD-3-Clause 112 6 11 Updated Feb 24, 2026
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 2 1 0 Updated Feb 24, 2026
  • seqr-helm Public

    Helm charts for the seqr project

    broadinstitute/seqr-helm’s past year of commit activity
    Python 3 BSD-3-Clause 5 5 2 Updated Feb 24, 2026
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 73 30 22 19 Updated Feb 24, 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 1 1 9 Updated Feb 24, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,913 623 1,279 (8 issues need help) 147 Updated Feb 24, 2026
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 200 AGPL-3.0 93 43 7 Updated Feb 24, 2026
  • permutect Public

    Permutect, an incredibly efficient deep learning architecture for somatic and germline variant calling

    broadinstitute/permutect’s past year of commit activity
    Python 9 1 10 2 Updated Feb 24, 2026
  • cellpainting-gallery Public

    Cell Painting Gallery

    broadinstitute/cellpainting-gallery’s past year of commit activity
    122 16 11 5 Updated Feb 24, 2026
  • depmap-omics-wgs Public
    broadinstitute/depmap-omics-wgs’s past year of commit activity
    Python 1 0 3 0 Updated Feb 24, 2026
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