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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 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 1k 377

Repositories

Showing 10 of 1443 repositories
  • viral-ngs Public

    viral-ngs: command line tools and wrappers for processing raw viral genomic data

    broadinstitute/viral-ngs’s past year of commit activity
    Python 193 MIT 67 3 1 Updated Feb 4, 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 96 26 Updated Feb 4, 2026
  • permutect Public

    Permutect, an incredibly efficient deep learning architecture for somatic and germline variant calling

    broadinstitute/permutect’s past year of commit activity
    Python 8 1 10 2 Updated Feb 4, 2026
  • seqr-helm Public

    Helm charts for the seqr project

    broadinstitute/seqr-helm’s past year of commit activity
    Python 3 BSD-3-Clause 5 4 1 Updated Feb 4, 2026
  • genomeshader Public

    Visualization of biobank-scale genomic datasets.

    broadinstitute/genomeshader’s past year of commit activity
    JavaScript 4 BSD-3-Clause 0 7 (2 issues need help) 3 Updated Feb 4, 2026
  • seqr-loading-pipelines Public

    hail-based pipelines for annotating variant callsets and exporting them to elasticsearch

    broadinstitute/seqr-loading-pipelines’s past year of commit activity
    Python 23 MIT 23 21 4 Updated Feb 4, 2026
  • pyqtl Public

    Collection of analysis tools for quantitative trait loci

    broadinstitute/pyqtl’s past year of commit activity
    Python 61 BSD-3-Clause 11 0 2 Updated Feb 4, 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 1 1 4 Updated Feb 3, 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 3, 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 44 5 Updated Feb 3, 2026
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