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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 1.9k 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 382

  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 1472 repositories
  • popout Public

    GPU-accelerated local ancestry inference at biobank scale, no reference panel required.

    broadinstitute/popout’s past year of commit activity
    Python 2 0 0 0 Updated Apr 20, 2026
  • glama Public

    Genomic long-read analysis modules and applications

    broadinstitute/glama’s past year of commit activity
    Rust 0 BSD-3-Clause 0 0 2 Updated Apr 20, 2026
  • jump-profiling-recipe Public

    Workflow for processing cpg0016-jump profiles

    broadinstitute/jump-profiling-recipe’s past year of commit activity
    Python 4 BSD-3-Clause 8 9 1 Updated Apr 20, 2026
  • carpenter-singh-lab-guide Public
    broadinstitute/carpenter-singh-lab-guide’s past year of commit activity
    1 BSD-3-Clause 0 3 1 Updated Apr 20, 2026
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 202 BSD-3-Clause 76 98 30 Updated Apr 20, 2026
  • EmmaEmb Public
    broadinstitute/EmmaEmb’s past year of commit activity
    Python 17 MIT 4 0 1 Updated Apr 20, 2026
  • BE3D Public

    BE3D public repository

    broadinstitute/BE3D’s past year of commit activity
    Python 1 MIT 0 2 0 Updated Apr 20, 2026
  • gene-lookup Public

    Website displaying aggregated info about gene-disease relationships @ genelookup.broadinstitute.org

    broadinstitute/gene-lookup’s past year of commit activity
    HTML 0 MIT 0 0 0 Updated Apr 20, 2026
  • bits-appengine Public

    BITS AppEngine Python Package

    broadinstitute/bits-appengine’s past year of commit activity
    Python 0 0 0 1 Updated Apr 20, 2026
  • sherlock Public

    DSP DevOps's deployment source-of-truth service

    broadinstitute/sherlock’s past year of commit activity
    Go 1 BSD-3-Clause 0 0 24 Updated Apr 20, 2026
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