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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 622

  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 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 1443 repositories
  • SpliceAI-lookup Public

    Website for checking a variant's SpliceAI, Pangolin, and other scores:

    broadinstitute/SpliceAI-lookup’s past year of commit activity
    HTML 27 MIT 10 7 0 Updated Feb 8, 2026
  • SpliceAI-lookup-dev Public

    dev UIs for spliceai-lookup.broadinstitute.org

    broadinstitute/SpliceAI-lookup-dev’s past year of commit activity
    HTML 0 MIT 0 0 0 Updated Feb 8, 2026
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 201 BSD-3-Clause 76 97 25 Updated Feb 8, 2026
  • bican-mccarroll-manuscript1 Public

    Scripts used to process data for the first McCarroll lab BICAN manuscript

    broadinstitute/bican-mccarroll-manuscript1’s past year of commit activity
    R 0 MIT 0 0 2 Updated Feb 8, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,906 622 1,275 (8 issues need help) 143 Updated Feb 8, 2026
  • TRExplorer Public

    An online portal for exploring tandem repeats (TRs) genome-wide.

    broadinstitute/TRExplorer’s past year of commit activity
    HTML 1 MIT 0 8 0 Updated Feb 8, 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 45 9 Updated Feb 8, 2026
  • poolq Public

    The Genetic Perturbation Platform's tool for deconvoluting and quantifying the results of pooled screens

    broadinstitute/poolq’s past year of commit activity
    Scala 5 1 8 (1 issue needs help) 1 Updated Feb 8, 2026
  • virnucpro-broad Public

    This is a custom-version of the VirNucPro tool that has been re-factored to be a more robust/production ready for usage at the Broad.

    broadinstitute/virnucpro-broad’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Feb 8, 2026
  • BE3D Public

    BE3D public repository

    broadinstitute/BE3D’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Feb 7, 2026
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