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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 606

  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 378

  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 371

Repositories

Showing 10 of 1391 repositories
  • hidive Public
    broadinstitute/hidive’s past year of commit activity
    Rust 0 BSD-3-Clause 0 6 1 Updated Jul 8, 2025
  • str-analysis Public

    Scripts and utilities related to analyzing short tandem repeats (STRs).

    broadinstitute/str-analysis’s past year of commit activity
    Python 38 MIT 9 0 0 Updated Jul 8, 2025
  • celldega Public

    Spatial omics analysis and visualization library

    broadinstitute/celldega’s past year of commit activity
    Jupyter Notebook 9 0 1 39 Updated Jul 8, 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 4 Updated Jul 8, 2025
  • 2022_09_07_New_phenotypic_dye_testing_CDoT_Broad_Analysis Public
    broadinstitute/2022_09_07_New_phenotypic_dye_testing_CDoT_Broad_Analysis’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 0 0 0 Updated Jul 8, 2025
  • gatk-sv Public

    A structural variation pipeline for short-read sequencing

    broadinstitute/gatk-sv’s past year of commit activity
    Python 189 BSD-3-Clause 75 83 28 Updated Jul 7, 2025
  • dcc_pigean_flask Public

    Flask server for the Pigean method

    broadinstitute/dcc_pigean_flask’s past year of commit activity
    Python 0 0 3 8 Updated Jul 7, 2025
  • dig-dug-portal Public
    broadinstitute/dig-dug-portal’s past year of commit activity
    Vue 2 BSD-3-Clause 2 1 0 Updated Jul 7, 2025
  • poasta Public

    Fast and exact gap-affine partial order alignment

    broadinstitute/poasta’s past year of commit activity
    Rust 52 BSD-3-Clause 5 12 4 Updated Jul 7, 2025
  • glama Public

    Genomic long-read analysis modules and applications

    broadinstitute/glama’s past year of commit activity
    Rust 0 BSD-3-Clause 0 0 2 Updated Jul 7, 2025
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