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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 625

  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 385

  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 1535 repositories
  • genomeshader Public

    Visualization of biobank-scale genomic datasets.

    broadinstitute/genomeshader's past year of commit activity
    JavaScript 6 BSD-3-Clause 0 9 (1 issue needs help) 3 Updated Sep 10, 2026
  • nf-send-mail-example Public
    broadinstitute/nf-send-mail-example's past year of commit activity
    Nextflow 0 0 0 0 Updated Sep 10, 2026
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv's past year of commit activity
    Python 207 BSD-3-Clause 82 100 28 Updated Sep 9, 2026
  • genohype-docs Public

    Documentation site for the genohype genomic data toolkit ecosystem

    broadinstitute/genohype-docs's past year of commit activity
    Astro 0 0 0 9 Updated Sep 10, 2026
  • exome-results-browsers Public

    Results browsers for case-control studies of psychiatric diseases done at the Broad Institute

    broadinstitute/exome-results-browsers's past year of commit activity
    TypeScript 12 BSD-3-Clause 4 7 9 Updated Sep 10, 2026
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines's past year of commit activity
    WDL 75 30 21 15 Updated Sep 9, 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 3 Updated Sep 9, 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 9, 2026
  • dig-artifact-provenance Public
    broadinstitute/dig-artifact-provenance's past year of commit activity
    Python 0 MIT 0 0 0 Updated Sep 9, 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 7 Updated Sep 9, 2026
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