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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 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
  • 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 23, 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) 2 Updated Feb 23, 2026
  • Himito Public
    broadinstitute/Himito’s past year of commit activity
    WDL 9 MIT 1 0 0 Updated Feb 23, 2026
  • bits-appengine Public

    BITS AppEngine Python Package

    broadinstitute/bits-appengine’s past year of commit activity
    Python 0 0 0 3 Updated Feb 23, 2026
  • protigy-v2 Public

    ProTIGY - Proteogenomics Toolset for Integrative Data Analysis

    broadinstitute/protigy-v2’s past year of commit activity
    R 3 BSD-3-Clause 1 10 1 Updated Feb 23, 2026
  • jump_hub Public

    The one-stop-shop for Morphological Profiling and JUMP Cell-Painting

    broadinstitute/jump_hub’s past year of commit activity
    Python 7 CC0-1.0 2 8 0 Updated Feb 23, 2026
  • long-read-pipelines Public

    Long read production pipelines

    broadinstitute/long-read-pipelines’s past year of commit activity
    Jupyter Notebook 151 BSD-3-Clause 25 95 (2 issues need help) 25 Updated Feb 23, 2026
  • monorepo Public

    Compendium of tools for the Imaging Platform

    broadinstitute/monorepo’s past year of commit activity
    Python 15 BSD-3-Clause 5 0 2 Updated Feb 22, 2026
  • cromwell Public

    Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

    broadinstitute/cromwell’s past year of commit activity
    Scala 1,053 BSD-3-Clause 378 759 50 Updated Feb 22, 2026
  • lrma-aou2-panel-creation Public Forked from broadinstitute/lrma-aou1-panel-creation

    Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 2 long-reads callset.

    broadinstitute/lrma-aou2-panel-creation’s past year of commit activity
    Java 0 2 0 2 Updated Feb 21, 2026
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