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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 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 1436 repositories
  • dig-job-server Public
    broadinstitute/dig-job-server’s past year of commit activity
    Vue 0 0 0 0 Updated Jan 7, 2026
  • seqr Public

    web-based analysis tool for rare disease genomics

    broadinstitute/seqr’s past year of commit activity
    Python 197 AGPL-3.0 92 49 7 Updated Jan 7, 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 Jan 7, 2026
  • seqr-helm Public

    Helm charts for the seqr project

    broadinstitute/seqr-helm’s past year of commit activity
    Python 3 BSD-3-Clause 3 4 1 Updated Jan 7, 2026
  • viral-pipelines Public

    viral-ngs: complete pipelines

    broadinstitute/viral-pipelines’s past year of commit activity
    WDL 70 30 21 17 Updated Jan 7, 2026
  • genomeshader Public

    Visualization of biobank-scale genomic datasets.

    broadinstitute/genomeshader’s past year of commit activity
    HTML 4 BSD-3-Clause 0 7 (2 issues need help) 3 Updated Jan 7, 2026
  • MDL-workflows Public

    Workflow, utilities and other artefacts developed by or for the Methods Development Lab at the Broad Institute

    broadinstitute/MDL-workflows’s past year of commit activity
    WDL 5 4 1 0 Updated Jan 7, 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 22 21 4 Updated Jan 7, 2026
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 200 BSD-3-Clause 76 94 27 Updated Jan 7, 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 15 Updated Jan 7, 2026
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