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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 2k 627

  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 384

  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 381

Repositories

Showing 10 of 1539 repositories
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk's past year of commit activity
    Java 1,999 627 1,292 (8 issues need help) 164 Updated Sep 24, 2026
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv's past year of commit activity
    Python 208 BSD-3-Clause 82 101 32 Updated Sep 24, 2026
  • geneset-extractor-dev Public

    Geneset Extractor Development

    broadinstitute/geneset-extractor-dev's past year of commit activity
    Shell 0 MIT 6 2 8 Updated Sep 24, 2026
  • gnomad_methods Public

    Hail helper functions for the gnomAD project and Translational Genomics Group

    broadinstitute/gnomad_methods's past year of commit activity
    Python 102 MIT 32 8 11 Updated Sep 23, 2026
  • molecular-data-provider Public

    Molecular Data Provider

    broadinstitute/molecular-data-provider's past year of commit activity
    Python 10 MIT 8 4 5 Updated Sep 23, 2026
  • lrma-sv-imputation-utils Public
    broadinstitute/lrma-sv-imputation-utils's past year of commit activity
    Rust 0 1 2 5 Updated Sep 23, 2026
  • dig-bioindex Public

    BIO index for genetic records stored in S3 and FastAPI server.

    broadinstitute/dig-bioindex's past year of commit activity
    Python 7 BSD-3-Clause 7 0 7 Updated Sep 23, 2026
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal's past year of commit activity
    Vue 3 BSD-3-Clause 3 0 14 Updated Sep 23, 2026
  • 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 2 Updated Sep 23, 2026
  • gnomad_qc Public
    broadinstitute/gnomad_qc's past year of commit activity
    Jupyter Notebook 70 BSD-3-Clause 31 5 17 Updated Sep 23, 2026
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