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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 Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,800 602 1,247 (8 issues need help) 137 Updated May 6, 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
  • 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 51 Updated May 5, 2025
  • ygramul Public

    Hierarchical knowledge graph for PIGEAN results

    broadinstitute/ygramul’s past year of commit activity
    Rust 0 BSD-3-Clause 0 0 0 Updated May 5, 2025
  • smaht-metadata-generator Public

    Pipeline to generate standardized metadata sheets for SMaHT sequencing projects

    broadinstitute/smaht-metadata-generator’s past year of commit activity
    Python 0 0 0 1 Updated May 5, 2025
  • broad-epi-workflows-collection Public

    This repo contains WDL workflows written by the Epigenomics program.

    broadinstitute/broad-epi-workflows-collection’s past year of commit activity
    Jupyter Notebook 1 MIT 1 0 0 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 14 Updated May 5, 2025
  • rawls Public

    Rawls service for DSDE

    broadinstitute/rawls’s past year of commit activity
    Scala 25 BSD-3-Clause 4 0 5 Updated May 5, 2025
  • 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
  • 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
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