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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 1.8k 602

  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 374

  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 363

Repositories

Showing 10 of 1377 repositories
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 187 BSD-3-Clause 75 81 23 Updated May 5, 2025
  • depmap-portal Public

    Code for the DepMap portal at depmap.org

    broadinstitute/depmap-portal’s past year of commit activity
    Python 8 BSD-2-Clause 1 0 15 Updated May 5, 2025
  • gnomad-blog Public

    Blog for the gnomAD project

    broadinstitute/gnomad-blog’s past year of commit activity
    JavaScript 4 BSD-3-Clause 0 7 3 Updated May 5, 2025
  • celldega Public

    Spatial omics analysis and visualization library

    broadinstitute/celldega’s past year of commit activity
    Jupyter Notebook 5 0 1 16 Updated May 5, 2025
  • 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 1,016 BSD-3-Clause 363 746 50 Updated May 5, 2025
  • idmp-fungal-pipelines Public
    broadinstitute/idmp-fungal-pipelines’s past year of commit activity
    WDL 0 GPL-3.0 0 0 1 Updated May 5, 2025
  • depmap-omics-wgs Public
    broadinstitute/depmap-omics-wgs’s past year of commit activity
    Python 0 0 3 0 Updated May 5, 2025
  • backstage Public

    Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)

    broadinstitute/backstage’s past year of commit activity
    TypeScript 2 0 0 5 Updated May 5, 2025
  • ml4h Public
    broadinstitute/ml4h’s past year of commit activity
    Python 132 25 30 (1 issue needs help) 24 Updated May 5, 2025
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 1 1 0 Updated May 5, 2025
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