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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 603

  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 373

  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 361

Repositories

Showing 10 of 1362 repositories
  • Methyl-CODEC Public
    broadinstitute/Methyl-CODEC’s past year of commit activity
    C++ 0 0 0 0 Updated Apr 2, 2025
  • juniper-analyses Public

    Code to run analyses and generate figures for JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale

    broadinstitute/juniper-analyses’s past year of commit activity
    R 0 0 0 0 Updated Apr 2, 2025
  • long-read-pipelines Public

    Long read production pipelines

    broadinstitute/long-read-pipelines’s past year of commit activity
    Jupyter Notebook 144 BSD-3-Clause 25 95 (2 issues need help) 26 Updated Apr 2, 2025
  • celldega Public

    Spatial omics analysis and visualization library

    broadinstitute/celldega’s past year of commit activity
    Jupyter Notebook 5 0 1 13 Updated Apr 1, 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 6 Updated Apr 1, 2025
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 1 1 0 Updated Apr 1, 2025
  • 2025_Grigoryan_Proteomics Public

    Repo for analysis of the Nomic Bio proteomics pilot data, collected as part of the OASIS Consortium

    broadinstitute/2025_Grigoryan_Proteomics’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 2 4 0 Updated Apr 1, 2025
  • gatk Public

    Official code repository for GATK versions 4 and up

    broadinstitute/gatk’s past year of commit activity
    Java 1,786 603 1,239 (8 issues need help) 138 Updated Apr 1, 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 1,011 BSD-3-Clause 361 745 50 Updated Apr 1, 2025
  • bosporus Public

    Experiments in interacting with generative AI

    broadinstitute/bosporus’s past year of commit activity
    Rust 0 BSD-3-Clause 0 0 0 Updated Apr 1, 2025
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