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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 626

  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 1536 repositories
  • Himito Public
    broadinstitute/Himito's past year of commit activity
    Rust 12 MIT 4 0 0 Updated Sep 15, 2026
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk's past year of commit activity
    Java 1,998 626 1,292 (8 issues need help) 154 Updated Sep 15, 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 15, 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 Sep 15, 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 15 13 Updated Sep 15, 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 29 Updated Sep 14, 2026
  • warp Public

    Warp Analysis Research Pipelines

    broadinstitute/warp's past year of commit activity
    Jupyter Notebook 230 BSD-3-Clause 118 13 20 Updated Sep 15, 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 2 Updated Sep 15, 2026
  • str-analysis Public

    Scripts and utilities for analyzing tandem repeats (TRs).

    broadinstitute/str-analysis's past year of commit activity
    Python 52 MIT 15 0 0 Updated Sep 14, 2026
  • colab-repeat-finder Public

    A tool for finding perfect repeats that span more than M base pairs and/or N repeats in the reference genome

    broadinstitute/colab-repeat-finder's past year of commit activity
    Python 2 MIT 0 0 0 Updated Sep 14, 2026
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